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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs1485218475

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr16:725177 (GRCh38.p14) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000004 (1/249132, GnomAD_exome)
T=0.0001 (1/8988, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CCDC78 : Synonymous Variant
HAGHL : 2KB Upstream Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 8988 C=0.9999 T=0.0001 0.999777 0.0 0.000223 0
European Sub 6062 C=0.9998 T=0.0002 0.99967 0.0 0.00033 0
African Sub 594 C=1.000 T=0.000 1.0 0.0 0.0 N/A
African Others Sub 8 C=1.0 T=0.0 1.0 0.0 0.0 N/A
African American Sub 586 C=1.000 T=0.000 1.0 0.0 0.0 N/A
Asian Sub 56 C=1.00 T=0.00 1.0 0.0 0.0 N/A
East Asian Sub 26 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 30 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 0 C=0 T=0 0 0 0 N/A
Latin American 2 Sub 0 C=0 T=0 0 0 0 N/A
South Asian Sub 0 C=0 T=0 0 0 0 N/A
Other Sub 2276 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 249132 C=0.999996 T=0.000004
gnomAD - Exomes European Sub 133572 C=0.999993 T=0.000007
gnomAD - Exomes Asian Sub 48974 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34562 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 15948 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 9992 C=1.0000 T=0.0000
gnomAD - Exomes Other Sub 6084 C=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 8988 C=0.9999 T=0.0001
Allele Frequency Aggregator European Sub 6062 C=0.9998 T=0.0002
Allele Frequency Aggregator Other Sub 2276 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 594 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 56 C=1.00 T=0.00
Allele Frequency Aggregator Latin American 1 Sub 0 C=0 T=0
Allele Frequency Aggregator Latin American 2 Sub 0 C=0 T=0
Allele Frequency Aggregator South Asian Sub 0 C=0 T=0
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p14 chr 16 NC_000016.10:g.725177C>T
GRCh37.p13 chr 16 NC_000016.9:g.775177C>T
CCDC78 RefSeqGene (LRG_705) NG_032932.1:g.6297G>A
Gene: CCDC78, coiled-coil domain containing 78 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CCDC78 transcript variant 1 NM_001031737.3:c.493-32G>A N/A Intron Variant
CCDC78 transcript variant 3 NM_001378030.1:c.493-32G>A N/A Intron Variant
CCDC78 transcript variant 4 NM_001378031.1:c.493-32G>A N/A Intron Variant
CCDC78 transcript variant 5 NM_001378033.1:c.99G>A G [GGG] > G [GGA] Coding Sequence Variant
coiled-coil domain-containing protein 78 isoform 5 NP_001364962.1:p.Gly33= G (Gly) > G (Gly) Synonymous Variant
CCDC78 transcript variant 6 NR_165382.1:n. N/A Intron Variant
CCDC78 transcript variant 7 NR_165383.1:n. N/A Intron Variant
CCDC78 transcript variant 8 NR_165384.1:n. N/A Intron Variant
CCDC78 transcript variant 9 NR_165385.1:n. N/A Intron Variant
CCDC78 transcript variant 10 NR_165386.1:n. N/A Intron Variant
CCDC78 transcript variant X13 XM_006720838.2:c.715-32G>A N/A Intron Variant
CCDC78 transcript variant X18 XM_006720843.5:c.493-32G>A N/A Intron Variant
CCDC78 transcript variant X2 XM_011522357.2:c.928-32G>A N/A Intron Variant
CCDC78 transcript variant X5 XM_011522360.2:c.895-32G>A N/A Intron Variant
CCDC78 transcript variant X16 XM_011522368.2:c.547-32G>A N/A Intron Variant
CCDC78 transcript variant X14 XM_047433602.1:c.715-32G>A N/A Intron Variant
CCDC78 transcript variant X23 XM_047433606.1:c.40-32G>A N/A Intron Variant
CCDC78 transcript variant X1 XM_011522356.2:c.987G>A G [GGG] > G [GGA] Coding Sequence Variant
coiled-coil domain-containing protein 78 isoform X1 XP_011520658.1:p.Gly329= G (Gly) > G (Gly) Synonymous Variant
CCDC78 transcript variant X3 XM_011522358.3:c.987G>A G [GGG] > G [GGA] Coding Sequence Variant
coiled-coil domain-containing protein 78 isoform X3 XP_011520660.1:p.Gly329= G (Gly) > G (Gly) Synonymous Variant
CCDC78 transcript variant X4 XM_011522359.2:c.954G>A G [GGG] > G [GGA] Coding Sequence Variant
coiled-coil domain-containing protein 78 isoform X4 XP_011520661.1:p.Gly318= G (Gly) > G (Gly) Synonymous Variant
CCDC78 transcript variant X6 XM_011522361.2:c.987G>A G [GGG] > G [GGA] Coding Sequence Variant
coiled-coil domain-containing protein 78 isoform X6 XP_011520663.1:p.Gly329= G (Gly) > G (Gly) Synonymous Variant
CCDC78 transcript variant X7 XM_017022929.2:c.987G>A G [GGG] > G [GGA] Coding Sequence Variant
coiled-coil domain-containing protein 78 isoform X7 XP_016878418.1:p.Gly329= G (Gly) > G (Gly) Synonymous Variant
CCDC78 transcript variant X8 XM_011522362.2:c.987G>A G [GGG] > G [GGA] Coding Sequence Variant
coiled-coil domain-containing protein 78 isoform X8 XP_011520664.1:p.Gly329= G (Gly) > G (Gly) Synonymous Variant
CCDC78 transcript variant X9 XM_011522363.2:c.987G>A G [GGG] > G [GGA] Coding Sequence Variant
coiled-coil domain-containing protein 78 isoform X9 XP_011520665.1:p.Gly329= G (Gly) > G (Gly) Synonymous Variant
CCDC78 transcript variant X10 XM_011522364.2:c.987G>A G [GGG] > G [GGA] Coding Sequence Variant
coiled-coil domain-containing protein 78 isoform X10 XP_011520666.1:p.Gly329= G (Gly) > G (Gly) Synonymous Variant
CCDC78 transcript variant X11 XM_011522365.2:c.774G>A G [GGG] > G [GGA] Coding Sequence Variant
coiled-coil domain-containing protein 78 isoform X11 XP_011520667.1:p.Gly258= G (Gly) > G (Gly) Synonymous Variant
CCDC78 transcript variant X12 XM_011522366.2:c.765G>A G [GGG] > G [GGA] Coding Sequence Variant
coiled-coil domain-containing protein 78 isoform X12 XP_011520668.1:p.Gly255= G (Gly) > G (Gly) Synonymous Variant
CCDC78 transcript variant X15 XM_011522367.2:c.606G>A G [GGG] > G [GGA] Coding Sequence Variant
coiled-coil domain-containing protein 78 isoform X15 XP_011520669.1:p.Gly202= G (Gly) > G (Gly) Synonymous Variant
CCDC78 transcript variant X17 XM_011522369.2:c.552G>A G [GGG] > G [GGA] Coding Sequence Variant
coiled-coil domain-containing protein 78 isoform X17 XP_011520671.1:p.Gly184= G (Gly) > G (Gly) Synonymous Variant
CCDC78 transcript variant X19 XM_047433603.1:c.468G>A G [GGG] > G [GGA] Coding Sequence Variant
coiled-coil domain-containing protein 78 isoform X19 XP_047289559.1:p.Gly156= G (Gly) > G (Gly) Synonymous Variant
CCDC78 transcript variant X20 XM_011522370.2:c.384G>A G [GGG] > G [GGA] Coding Sequence Variant
coiled-coil domain-containing protein 78 isoform X20 XP_011520672.1:p.Gly128= G (Gly) > G (Gly) Synonymous Variant
CCDC78 transcript variant X21 XM_047433604.1:c.468G>A G [GGG] > G [GGA] Coding Sequence Variant
coiled-coil domain-containing protein 78 isoform X19 XP_047289560.1:p.Gly156= G (Gly) > G (Gly) Synonymous Variant
CCDC78 transcript variant X22 XM_047433605.1:c.99G>A G [GGG] > G [GGA] Coding Sequence Variant
coiled-coil domain-containing protein 78 isoform X21 XP_047289561.1:p.Gly33= G (Gly) > G (Gly) Synonymous Variant
CCDC78 transcript variant X24 XM_047433607.1:c.519G>A G [GGG] > G [GGA] Coding Sequence Variant
coiled-coil domain-containing protein 78 isoform X23 XP_047289563.1:p.Gly173= G (Gly) > G (Gly) Synonymous Variant
Gene: HAGHL, hydroxyacylglutathione hydrolase like (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
HAGHL transcript variant 3 NM_001290137.2:c. N/A Upstream Transcript Variant
HAGHL transcript variant 4 NM_001290139.2:c. N/A Upstream Transcript Variant
HAGHL transcript variant 5 NM_001323635.2:c. N/A Upstream Transcript Variant
HAGHL transcript variant 6 NM_001323636.2:c. N/A Upstream Transcript Variant
HAGHL transcript variant 7 NM_001365282.1:c. N/A Upstream Transcript Variant
HAGHL transcript variant 2 NM_032304.4:c. N/A Upstream Transcript Variant
HAGHL transcript variant X1 XM_005255631.5:c. N/A Upstream Transcript Variant
HAGHL transcript variant X5 XM_005255632.2:c. N/A Upstream Transcript Variant
HAGHL transcript variant X2 XM_011522712.2:c. N/A Upstream Transcript Variant
HAGHL transcript variant X1 XM_047434792.1:c. N/A Upstream Transcript Variant
HAGHL transcript variant X3 XM_047434794.1:c. N/A Upstream Transcript Variant
HAGHL transcript variant X4 XM_047434795.1:c. N/A Upstream Transcript Variant
HAGHL transcript variant X6 XM_047434796.1:c. N/A Upstream Transcript Variant
HAGHL transcript variant X7 XM_047434797.1:c. N/A Upstream Transcript Variant
HAGHL transcript variant X8 XM_047434798.1:c. N/A Upstream Transcript Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement C= T
GRCh38.p14 chr 16 NC_000016.10:g.725177= NC_000016.10:g.725177C>T
GRCh37.p13 chr 16 NC_000016.9:g.775177= NC_000016.9:g.775177C>T
CCDC78 RefSeqGene (LRG_705) NG_032932.1:g.6297= NG_032932.1:g.6297G>A
CCDC78 transcript variant 5 NM_001378033.1:c.99= NM_001378033.1:c.99G>A
CCDC78 transcript variant X3 XM_011522358.3:c.987= XM_011522358.3:c.987G>A
CCDC78 transcript variant X3 XM_011522358.2:c.987= XM_011522358.2:c.987G>A
CCDC78 transcript variant X3 XM_011522358.1:c.987= XM_011522358.1:c.987G>A
CCDC78 transcript variant X8 XM_011522362.2:c.987= XM_011522362.2:c.987G>A
CCDC78 transcript variant X8 XM_011522362.1:c.987= XM_011522362.1:c.987G>A
CCDC78 transcript variant X1 XM_011522356.2:c.987= XM_011522356.2:c.987G>A
CCDC78 transcript variant X1 XM_011522356.1:c.987= XM_011522356.1:c.987G>A
CCDC78 transcript variant X4 XM_011522359.2:c.954= XM_011522359.2:c.954G>A
CCDC78 transcript variant X4 XM_011522359.1:c.954= XM_011522359.1:c.954G>A
CCDC78 transcript variant X6 XM_011522361.2:c.987= XM_011522361.2:c.987G>A
CCDC78 transcript variant X6 XM_011522361.1:c.987= XM_011522361.1:c.987G>A
CCDC78 transcript variant X9 XM_011522363.2:c.987= XM_011522363.2:c.987G>A
CCDC78 transcript variant X9 XM_011522363.1:c.987= XM_011522363.1:c.987G>A
CCDC78 transcript variant X7 XM_017022929.2:c.987= XM_017022929.2:c.987G>A
CCDC78 transcript variant X7 XM_017022929.1:c.987= XM_017022929.1:c.987G>A
CCDC78 transcript variant X10 XM_011522364.2:c.987= XM_011522364.2:c.987G>A
CCDC78 transcript variant X10 XM_011522364.1:c.987= XM_011522364.1:c.987G>A
CCDC78 transcript variant X11 XM_011522365.2:c.774= XM_011522365.2:c.774G>A
CCDC78 transcript variant X11 XM_011522365.1:c.774= XM_011522365.1:c.774G>A
CCDC78 transcript variant X12 XM_011522366.2:c.765= XM_011522366.2:c.765G>A
CCDC78 transcript variant X12 XM_011522366.1:c.765= XM_011522366.1:c.765G>A
CCDC78 transcript variant X15 XM_011522367.2:c.606= XM_011522367.2:c.606G>A
CCDC78 transcript variant X14 XM_011522367.1:c.606= XM_011522367.1:c.606G>A
CCDC78 transcript variant X17 XM_011522369.2:c.552= XM_011522369.2:c.552G>A
CCDC78 transcript variant X16 XM_011522369.1:c.552= XM_011522369.1:c.552G>A
CCDC78 transcript variant X20 XM_011522370.2:c.384= XM_011522370.2:c.384G>A
CCDC78 transcript variant X18 XM_011522370.1:c.384= XM_011522370.1:c.384G>A
CCDC78 transcript variant 2 NM_173476.2:c.774= NM_173476.2:c.774G>A
FLJ34512 transcript NM_173476.1:c.552= NM_173476.1:c.552G>A
CCDC78 transcript variant X19 XM_047433603.1:c.468= XM_047433603.1:c.468G>A
CCDC78 transcript variant X21 XM_047433604.1:c.468= XM_047433604.1:c.468G>A
CCDC78 transcript variant X22 XM_047433605.1:c.99= XM_047433605.1:c.99G>A
CCDC78 transcript variant X24 XM_047433607.1:c.519= XM_047433607.1:c.519G>A
coiled-coil domain-containing protein 78 isoform 5 NP_001364962.1:p.Gly33= NP_001364962.1:p.Gly33=
coiled-coil domain-containing protein 78 isoform X3 XP_011520660.1:p.Gly329= XP_011520660.1:p.Gly329=
coiled-coil domain-containing protein 78 isoform X8 XP_011520664.1:p.Gly329= XP_011520664.1:p.Gly329=
coiled-coil domain-containing protein 78 isoform X1 XP_011520658.1:p.Gly329= XP_011520658.1:p.Gly329=
coiled-coil domain-containing protein 78 isoform X4 XP_011520661.1:p.Gly318= XP_011520661.1:p.Gly318=
coiled-coil domain-containing protein 78 isoform X6 XP_011520663.1:p.Gly329= XP_011520663.1:p.Gly329=
coiled-coil domain-containing protein 78 isoform X9 XP_011520665.1:p.Gly329= XP_011520665.1:p.Gly329=
coiled-coil domain-containing protein 78 isoform X7 XP_016878418.1:p.Gly329= XP_016878418.1:p.Gly329=
coiled-coil domain-containing protein 78 isoform X10 XP_011520666.1:p.Gly329= XP_011520666.1:p.Gly329=
coiled-coil domain-containing protein 78 isoform X11 XP_011520667.1:p.Gly258= XP_011520667.1:p.Gly258=
coiled-coil domain-containing protein 78 isoform X12 XP_011520668.1:p.Gly255= XP_011520668.1:p.Gly255=
coiled-coil domain-containing protein 78 isoform X15 XP_011520669.1:p.Gly202= XP_011520669.1:p.Gly202=
coiled-coil domain-containing protein 78 isoform X17 XP_011520671.1:p.Gly184= XP_011520671.1:p.Gly184=
coiled-coil domain-containing protein 78 isoform X20 XP_011520672.1:p.Gly128= XP_011520672.1:p.Gly128=
coiled-coil domain-containing protein 78 isoform X19 XP_047289559.1:p.Gly156= XP_047289559.1:p.Gly156=
coiled-coil domain-containing protein 78 isoform X19 XP_047289560.1:p.Gly156= XP_047289560.1:p.Gly156=
coiled-coil domain-containing protein 78 isoform X21 XP_047289561.1:p.Gly33= XP_047289561.1:p.Gly33=
coiled-coil domain-containing protein 78 isoform X23 XP_047289563.1:p.Gly173= XP_047289563.1:p.Gly173=
CCDC78 transcript NM_001031737.2:c.493-32= NM_001031737.2:c.493-32G>A
CCDC78 transcript variant 1 NM_001031737.3:c.493-32= NM_001031737.3:c.493-32G>A
CCDC78 transcript variant 3 NM_001378030.1:c.493-32= NM_001378030.1:c.493-32G>A
CCDC78 transcript variant 4 NM_001378031.1:c.493-32= NM_001378031.1:c.493-32G>A
CCDC78 transcript variant X2 XM_005255101.1:c.895-32= XM_005255101.1:c.895-32G>A
CCDC78 transcript variant X3 XM_005255102.1:c.715-32= XM_005255102.1:c.715-32G>A
CCDC78 transcript variant X6 XM_005255105.1:c.493-32= XM_005255105.1:c.493-32G>A
CCDC78 transcript variant X8 XM_005255107.1:c.-402-32= XM_005255107.1:c.-402-32G>A
CCDC78 transcript variant X13 XM_006720838.2:c.715-32= XM_006720838.2:c.715-32G>A
CCDC78 transcript variant X18 XM_006720843.5:c.493-32= XM_006720843.5:c.493-32G>A
CCDC78 transcript variant X2 XM_011522357.2:c.928-32= XM_011522357.2:c.928-32G>A
CCDC78 transcript variant X5 XM_011522360.2:c.895-32= XM_011522360.2:c.895-32G>A
CCDC78 transcript variant X16 XM_011522368.2:c.547-32= XM_011522368.2:c.547-32G>A
CCDC78 transcript variant X14 XM_047433602.1:c.715-32= XM_047433602.1:c.715-32G>A
CCDC78 transcript variant X23 XM_047433606.1:c.40-32= XM_047433606.1:c.40-32G>A
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

1 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2741587577 Nov 08, 2017 (151)
2 gnomAD - Exomes NC_000016.9 - 775177 Jul 13, 2019 (153)
3 ALFA NC_000016.10 - 725177 Apr 26, 2021 (155)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
10858577, ss2741587577 NC_000016.9:775176:C:T NC_000016.10:725176:C:T (self)
5413571572 NC_000016.10:725176:C:T NC_000016.10:725176:C:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1485218475

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top▲ Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post820+afb47a3d