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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.

rs1474734240

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:40035469-40035470 (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
delA
Variation Type
Indel Insertion and Deletion
Frequency
delA=0.000004 (1/251314, GnomAD_exome)
delA=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ZNF780B : Frameshift 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 10680 AA=1.00000 A=0.00000 1.0 0.0 0.0 N/A
European Sub 6962 AA=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Sub 2294 AA=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 84 AA=1.00 A=0.00 1.0 0.0 0.0 N/A
African American Sub 2210 AA=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 AA=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 AA=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 AA=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 AA=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 AA=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 AA=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 466 AA=1.000 A=0.000 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 251314 AA=0.999996 delA=0.000004
gnomAD - Exomes European Sub 135330 AA=0.999993 delA=0.000007
gnomAD - Exomes Asian Sub 49004 AA=1.00000 delA=0.00000
gnomAD - Exomes American Sub 34588 AA=1.00000 delA=0.00000
gnomAD - Exomes African Sub 16190 AA=1.00000 delA=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10078 AA=1.00000 delA=0.00000
gnomAD - Exomes Other Sub 6124 AA=1.0000 delA=0.0000
Allele Frequency Aggregator Total Global 10680 AA=1.00000 delA=0.00000
Allele Frequency Aggregator European Sub 6962 AA=1.0000 delA=0.0000
Allele Frequency Aggregator African Sub 2294 AA=1.0000 delA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 AA=1.000 delA=0.000
Allele Frequency Aggregator Other Sub 466 AA=1.000 delA=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 AA=1.000 delA=0.000
Allele Frequency Aggregator Asian Sub 108 AA=1.000 delA=0.000
Allele Frequency Aggregator South Asian Sub 94 AA=1.00 delA=0.00
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 19 NC_000019.10:g.40035470del
GRCh37.p13 chr 19 NC_000019.9:g.40541377del
GRCh38.p14 chr 19 fix patch HG2021_PATCH NW_009646206.1:g.310613del
Gene: ZNF780B, zinc finger protein 780B (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ZNF780B transcript NM_001005851.3:c.1390del C [TGC] > A [GC] Coding Sequence Variant
zinc finger protein 780B NP_001005851.1:p.Cys464fs C (Cys) > A (Ala) Frameshift Variant
ZNF780B transcript variant X1 XM_006723072.5:c.1393del C [TGC] > A [GC] Coding Sequence Variant
zinc finger protein 780B isoform X1 XP_006723135.1:p.Cys465fs C (Cys) > A (Ala) Frameshift Variant
ZNF780B transcript variant X2 XM_005258591.6:c.1393del C [TGC] > A [GC] Coding Sequence Variant
zinc finger protein 780B isoform X1 XP_005258648.1:p.Cys465fs C (Cys) > A (Ala) Frameshift Variant
ZNF780B transcript variant X3 XM_047438337.1:c.1393del C [TGC] > A [GC] Coding Sequence Variant
zinc finger protein 780B isoform X1 XP_047294293.1:p.Cys465fs C (Cys) > A (Ala) Frameshift Variant
ZNF780B transcript variant X4 XM_005258595.4:c.1393del C [TGC] > A [GC] Coding Sequence Variant
zinc finger protein 780B isoform X1 XP_005258652.1:p.Cys465fs C (Cys) > A (Ala) Frameshift Variant
ZNF780B transcript variant X5 XM_005258590.5:c.1393del C [TGC] > A [GC] Coding Sequence Variant
zinc finger protein 780B isoform X1 XP_005258647.1:p.Cys465fs C (Cys) > A (Ala) Frameshift Variant
ZNF780B transcript variant X6 XM_005258592.4:c.1393del C [TGC] > A [GC] Coding Sequence Variant
zinc finger protein 780B isoform X1 XP_005258649.1:p.Cys465fs C (Cys) > A (Ala) Frameshift Variant
ZNF780B transcript variant X7 XM_011526593.3:c.1393del C [TGC] > A [GC] Coding Sequence Variant
zinc finger protein 780B isoform X1 XP_011524895.1:p.Cys465fs C (Cys) > A (Ala) Frameshift Variant
ZNF780B transcript variant X8 XM_047438338.1:c.1393del C [TGC] > A [GC] Coding Sequence Variant
zinc finger protein 780B isoform X1 XP_047294294.1:p.Cys465fs C (Cys) > A (Ala) Frameshift Variant
ZNF780B transcript variant X9 XM_005258593.3:c.1390del C [TGC] > A [GC] Coding Sequence Variant
zinc finger protein 780B isoform X2 XP_005258650.1:p.Cys464fs C (Cys) > A (Ala) Frameshift Variant
ZNF780B transcript variant X10 XM_017026425.3:c.1390del C [TGC] > A [GC] Coding Sequence Variant
zinc finger protein 780B isoform X2 XP_016881914.1:p.Cys464fs C (Cys) > A (Ala) Frameshift Variant
ZNF780B transcript variant X11 XM_047438339.1:c.1390del C [TGC] > A [GC] Coding Sequence Variant
zinc finger protein 780B isoform X2 XP_047294295.1:p.Cys464fs C (Cys) > A (Ala) Frameshift Variant
ZNF780B transcript variant X12 XM_047438340.1:c.1390del C [TGC] > A [GC] Coding Sequence Variant
zinc finger protein 780B isoform X2 XP_047294296.1:p.Cys464fs C (Cys) > A (Ala) Frameshift Variant
ZNF780B transcript variant X13 XM_017026426.2:c.1390del C [TGC] > A [GC] Coding Sequence Variant
zinc finger protein 780B isoform X2 XP_016881915.1:p.Cys464fs C (Cys) > A (Ala) Frameshift Variant
ZNF780B transcript variant X14 XM_047438341.1:c.1390del C [TGC] > A [GC] Coding Sequence Variant
zinc finger protein 780B isoform X2 XP_047294297.1:p.Cys464fs C (Cys) > A (Ala) Frameshift Variant
ZNF780B transcript variant X15 XM_017026427.2:c.1390del C [TGC] > A [GC] Coding Sequence Variant
zinc finger protein 780B isoform X2 XP_016881916.1:p.Cys464fs C (Cys) > A (Ala) Frameshift Variant
ZNF780B transcript variant X16 XM_047438342.1:c.1390del C [TGC] > A [GC] Coding Sequence Variant
zinc finger protein 780B isoform X2 XP_047294298.1:p.Cys464fs C (Cys) > A (Ala) Frameshift 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 AA= delA
GRCh38.p14 chr 19 NC_000019.10:g.40035469_40035470= NC_000019.10:g.40035470del
GRCh37.p13 chr 19 NC_000019.9:g.40541376_40541377= NC_000019.9:g.40541377del
GRCh38.p14 chr 19 fix patch HG2021_PATCH NW_009646206.1:g.310612_310613= NW_009646206.1:g.310613del
ZNF780B transcript variant X2 XM_005258591.6:c.1392_1393= XM_005258591.6:c.1393del
ZNF780B transcript variant X3 XM_005258591.5:c.1392_1393= XM_005258591.5:c.1393del
ZNF780B transcript variant X3 XM_005258591.4:c.1392_1393= XM_005258591.4:c.1393del
ZNF780B transcript variant X6 XM_005258591.3:c.1392_1393= XM_005258591.3:c.1393del
ZNF780B transcript variant X2 XM_005258591.2:c.1392_1393= XM_005258591.2:c.1393del
ZNF780B transcript variant X2 XM_005258591.1:c.1392_1393= XM_005258591.1:c.1393del
ZNF780B transcript variant X5 XM_005258590.5:c.1392_1393= XM_005258590.5:c.1393del
ZNF780B transcript variant X1 XM_005258590.4:c.1392_1393= XM_005258590.4:c.1393del
ZNF780B transcript variant X1 XM_005258590.3:c.1392_1393= XM_005258590.3:c.1393del
ZNF780B transcript variant X1 XM_005258590.2:c.1392_1393= XM_005258590.2:c.1393del
ZNF780B transcript variant X1 XM_005258590.1:c.1392_1393= XM_005258590.1:c.1393del
ZNF780B transcript variant X1 XM_006723072.5:c.1392_1393= XM_006723072.5:c.1393del
ZNF780B transcript variant X2 XM_006723072.4:c.1392_1393= XM_006723072.4:c.1393del
ZNF780B transcript variant X2 XM_006723072.3:c.1392_1393= XM_006723072.3:c.1393del
ZNF780B transcript variant X2 XM_006723072.2:c.1392_1393= XM_006723072.2:c.1393del
ZNF780B transcript variant X7 XM_006723072.1:c.1392_1393= XM_006723072.1:c.1393del
ZNF780B transcript variant X6 XM_005258592.4:c.1392_1393= XM_005258592.4:c.1393del
ZNF780B transcript variant X4 XM_005258592.3:c.1392_1393= XM_005258592.3:c.1393del
ZNF780B transcript variant X3 XM_005258592.2:c.1392_1393= XM_005258592.2:c.1393del
ZNF780B transcript variant X3 XM_005258592.1:c.1392_1393= XM_005258592.1:c.1393del
ZNF780B transcript variant X4 XM_005258595.4:c.1392_1393= XM_005258595.4:c.1393del
ZNF780B transcript variant X5 XM_005258595.3:c.1392_1393= XM_005258595.3:c.1393del
ZNF780B transcript variant X5 XM_005258595.2:c.1392_1393= XM_005258595.2:c.1393del
ZNF780B transcript variant X6 XM_005258595.1:c.1392_1393= XM_005258595.1:c.1393del
ZNF780B transcript variant X9 XM_005258593.3:c.1389_1390= XM_005258593.3:c.1390del
ZNF780B transcript variant X7 XM_005258593.2:c.1389_1390= XM_005258593.2:c.1390del
ZNF780B transcript variant X8 XM_005258593.1:c.1389_1390= XM_005258593.1:c.1390del
ZNF780B transcript variant X10 XM_017026425.3:c.1389_1390= XM_017026425.3:c.1390del
ZNF780B transcript variant X8 XM_017026425.2:c.1389_1390= XM_017026425.2:c.1390del
ZNF780B transcript variant X8 XM_017026425.1:c.1389_1390= XM_017026425.1:c.1390del
ZNF780B transcript variant X7 XM_011526593.3:c.1392_1393= XM_011526593.3:c.1393del
ZNF780B transcript variant X6 XM_011526593.2:c.1392_1393= XM_011526593.2:c.1393del
ZNF780B transcript variant X7 XM_011526593.1:c.1392_1393= XM_011526593.1:c.1393del
ZNF780B transcript NM_001005851.3:c.1389_1390= NM_001005851.3:c.1390del
ZNF780B transcript NM_001005851.2:c.1389_1390= NM_001005851.2:c.1390del
ZNF780B transcript variant X15 XM_017026427.2:c.1389_1390= XM_017026427.2:c.1390del
ZNF780B transcript variant X13 XM_017026427.1:c.1389_1390= XM_017026427.1:c.1390del
ZNF780B transcript variant X13 XM_017026426.2:c.1389_1390= XM_017026426.2:c.1390del
ZNF780B transcript variant X9 XM_017026426.1:c.1389_1390= XM_017026426.1:c.1390del
ZNF780B transcript variant X8 XM_047438338.1:c.1392_1393= XM_047438338.1:c.1393del
ZNF780B transcript variant X11 XM_047438339.1:c.1389_1390= XM_047438339.1:c.1390del
ZNF780B transcript variant X14 XM_047438341.1:c.1389_1390= XM_047438341.1:c.1390del
ZNF780B transcript variant X12 XM_047438340.1:c.1389_1390= XM_047438340.1:c.1390del
ZNF780B transcript variant X16 XM_047438342.1:c.1389_1390= XM_047438342.1:c.1390del
ZNF780B transcript variant X3 XM_047438337.1:c.1392_1393= XM_047438337.1:c.1393del
zinc finger protein 780B isoform X1 XP_005258648.1:p.His464_Cys465= XP_005258648.1:p.Cys465fs
zinc finger protein 780B isoform X1 XP_005258647.1:p.His464_Cys465= XP_005258647.1:p.Cys465fs
zinc finger protein 780B isoform X1 XP_006723135.1:p.His464_Cys465= XP_006723135.1:p.Cys465fs
zinc finger protein 780B isoform X1 XP_005258649.1:p.His464_Cys465= XP_005258649.1:p.Cys465fs
zinc finger protein 780B isoform X1 XP_005258652.1:p.His464_Cys465= XP_005258652.1:p.Cys465fs
zinc finger protein 780B isoform X2 XP_005258650.1:p.His463_Cys464= XP_005258650.1:p.Cys464fs
zinc finger protein 780B isoform X2 XP_016881914.1:p.His463_Cys464= XP_016881914.1:p.Cys464fs
zinc finger protein 780B isoform X1 XP_011524895.1:p.His464_Cys465= XP_011524895.1:p.Cys465fs
zinc finger protein 780B NP_001005851.1:p.His463_Cys464= NP_001005851.1:p.Cys464fs
zinc finger protein 780B isoform X2 XP_016881916.1:p.His463_Cys464= XP_016881916.1:p.Cys464fs
zinc finger protein 780B isoform X2 XP_016881915.1:p.His463_Cys464= XP_016881915.1:p.Cys464fs
zinc finger protein 780B isoform X1 XP_047294294.1:p.His464_Cys465= XP_047294294.1:p.Cys465fs
zinc finger protein 780B isoform X2 XP_047294295.1:p.His463_Cys464= XP_047294295.1:p.Cys464fs
zinc finger protein 780B isoform X2 XP_047294297.1:p.His463_Cys464= XP_047294297.1:p.Cys464fs
zinc finger protein 780B isoform X2 XP_047294296.1:p.His463_Cys464= XP_047294296.1:p.Cys464fs
zinc finger protein 780B isoform X2 XP_047294298.1:p.His463_Cys464= XP_047294298.1:p.Cys464fs
zinc finger protein 780B isoform X1 XP_047294293.1:p.His464_Cys465= XP_047294293.1:p.Cys465fs
ZNF780B transcript variant X5 XM_005258594.1:c.1390+3= XM_005258594.1:c.1390+3del
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 ss2743996116 Nov 08, 2017 (151)
2 gnomAD - Exomes NC_000019.9 - 40541376 Jul 13, 2019 (153)
3 ALFA NC_000019.10 - 40035469 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
13309918, ss2743996116 NC_000019.9:40541375:A: NC_000019.10:40035468:AA:A (self)
5367047017 NC_000019.10:40035468:AA:A NC_000019.10:40035468:AA:A (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 rs1474734240

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