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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.

rs1481932653

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:35667205 (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
A>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000004 (1/264690, TOPMED)
C=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SPEF2 : Missense 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 30412 A=0.99997 C=0.00003 0.999934 0.0 6.6e-05 0
European Sub 19780 A=0.99995 C=0.00005 0.999899 0.0 0.000101 0
African Sub 7736 A=1.0000 C=0.0000 1.0 0.0 0.0 N/A
African Others Sub 298 A=1.000 C=0.000 1.0 0.0 0.0 N/A
African American Sub 7438 A=1.0000 C=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 A=1.000 C=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 A=1.00 C=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 A=1.00 C=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 A=1.000 C=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 A=1.000 C=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 A=1.00 C=0.00 1.0 0.0 0.0 N/A
Other Sub 1930 A=1.0000 C=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
TopMed Global Study-wide 264690 A=0.999996 C=0.000004
Allele Frequency Aggregator Total Global 14050 A=1.00000 C=0.00000
Allele Frequency Aggregator European Sub 9690 A=1.0000 C=0.0000
Allele Frequency Aggregator African Sub 2898 A=1.0000 C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 A=1.000 C=0.000
Allele Frequency Aggregator Other Sub 496 A=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=1.000 C=0.000
Allele Frequency Aggregator Asian Sub 112 A=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 98 A=1.00 C=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 5 NC_000005.10:g.35667205A>C
GRCh37.p13 chr 5 NC_000005.9:g.35667307A>C
Gene: SPEF2, sperm flagellar 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SPEF2 transcript variant 1 NM_024867.4:c.1301A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform 1 NP_079143.3:p.Asp434Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant 2 NM_144722.4:c.1301A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform 2 NP_653323.1:p.Asp434Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant X1 XM_011514135.4:c.1301A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform X1 XP_011512437.1:p.Asp434Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant X2 XM_011514136.4:c.1301A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform X2 XP_011512438.1:p.Asp434Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant X3 XM_011514137.4:c.1301A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform X3 XP_011512439.1:p.Asp434Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant X4 XM_011514138.4:c.1301A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform X4 XP_011512440.1:p.Asp434Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant X5 XM_011514139.4:c.1301A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform X5 XP_011512441.1:p.Asp434Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant X6 XM_011514140.3:c.1130A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform X6 XP_011512442.1:p.Asp377Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant X7 XM_017009880.3:c.1130A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform X7 XP_016865369.1:p.Asp377Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant X8 XM_047417765.1:c.875A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform X8 XP_047273721.1:p.Asp292Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant X9 XM_047417766.1:c.875A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform X8 XP_047273722.1:p.Asp292Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant X10 XM_005248376.5:c.1301A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform X9 XP_005248433.1:p.Asp434Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant X11 XM_005248377.5:c.1301A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform X10 XP_005248434.1:p.Asp434Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant X13 XM_047417767.1:c.1301A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform X11 XP_047273723.1:p.Asp434Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant X14 XM_047417768.1:c.1301A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform X12 XP_047273724.1:p.Asp434Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant X15 XM_047417769.1:c.1301A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform X13 XP_047273725.1:p.Asp434Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant X16 XM_017009882.3:c.1301A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform X14 XP_016865371.1:p.Asp434Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant X17 XM_005248378.5:c.1301A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform X15 XP_005248435.1:p.Asp434Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant X18 XM_047417770.1:c.1301A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform X16 XP_047273726.1:p.Asp434Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant X19 XM_024446219.2:c.1130A>C D [GAT] > A [GCT] Coding Sequence Variant
sperm flagellar protein 2 isoform X17 XP_024301987.1:p.Asp377Ala D (Asp) > A (Ala) Missense Variant
SPEF2 transcript variant X12 XR_925655.3:n.1436A>C N/A Non Coding 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 A= C
GRCh38.p14 chr 5 NC_000005.10:g.35667205= NC_000005.10:g.35667205A>C
GRCh37.p13 chr 5 NC_000005.9:g.35667307= NC_000005.9:g.35667307A>C
SPEF2 transcript variant X10 XM_005248376.5:c.1301= XM_005248376.5:c.1301A>C
SPEF2 transcript variant X10 XM_005248376.4:c.1301= XM_005248376.4:c.1301A>C
SPEF2 transcript variant X10 XM_005248376.3:c.1301= XM_005248376.3:c.1301A>C
SPEF2 transcript variant X1 XM_005248376.2:c.1301= XM_005248376.2:c.1301A>C
SPEF2 transcript variant X1 XM_005248376.1:c.1301= XM_005248376.1:c.1301A>C
SPEF2 transcript variant X11 XM_005248377.5:c.1301= XM_005248377.5:c.1301A>C
SPEF2 transcript variant X11 XM_005248377.4:c.1301= XM_005248377.4:c.1301A>C
SPEF2 transcript variant X11 XM_005248377.3:c.1301= XM_005248377.3:c.1301A>C
SPEF2 transcript variant X9 XM_005248377.2:c.1301= XM_005248377.2:c.1301A>C
SPEF2 transcript variant X2 XM_005248377.1:c.1301= XM_005248377.1:c.1301A>C
SPEF2 transcript variant X17 XM_005248378.5:c.1301= XM_005248378.5:c.1301A>C
SPEF2 transcript variant X16 XM_005248378.4:c.1301= XM_005248378.4:c.1301A>C
SPEF2 transcript variant X17 XM_005248378.3:c.1301= XM_005248378.3:c.1301A>C
SPEF2 transcript variant X14 XM_005248378.2:c.1301= XM_005248378.2:c.1301A>C
SPEF2 transcript variant X3 XM_005248378.1:c.1301= XM_005248378.1:c.1301A>C
SPEF2 transcript variant X1 XM_011514135.4:c.1301= XM_011514135.4:c.1301A>C
SPEF2 transcript variant X1 XM_011514135.3:c.1301= XM_011514135.3:c.1301A>C
SPEF2 transcript variant X1 XM_011514135.2:c.1301= XM_011514135.2:c.1301A>C
SPEF2 transcript variant X1 XM_011514135.1:c.1301= XM_011514135.1:c.1301A>C
SPEF2 transcript variant X3 XM_011514137.4:c.1301= XM_011514137.4:c.1301A>C
SPEF2 transcript variant X3 XM_011514137.3:c.1301= XM_011514137.3:c.1301A>C
SPEF2 transcript variant X3 XM_011514137.2:c.1301= XM_011514137.2:c.1301A>C
SPEF2 transcript variant X3 XM_011514137.1:c.1301= XM_011514137.1:c.1301A>C
SPEF2 transcript variant X4 XM_011514138.4:c.1301= XM_011514138.4:c.1301A>C
SPEF2 transcript variant X4 XM_011514138.3:c.1301= XM_011514138.3:c.1301A>C
SPEF2 transcript variant X4 XM_011514138.2:c.1301= XM_011514138.2:c.1301A>C
SPEF2 transcript variant X4 XM_011514138.1:c.1301= XM_011514138.1:c.1301A>C
SPEF2 transcript variant X5 XM_011514139.4:c.1301= XM_011514139.4:c.1301A>C
SPEF2 transcript variant X5 XM_011514139.3:c.1301= XM_011514139.3:c.1301A>C
SPEF2 transcript variant X5 XM_011514139.2:c.1301= XM_011514139.2:c.1301A>C
SPEF2 transcript variant X5 XM_011514139.1:c.1301= XM_011514139.1:c.1301A>C
SPEF2 transcript variant X2 XM_011514136.4:c.1301= XM_011514136.4:c.1301A>C
SPEF2 transcript variant X2 XM_011514136.3:c.1301= XM_011514136.3:c.1301A>C
SPEF2 transcript variant X2 XM_011514136.2:c.1301= XM_011514136.2:c.1301A>C
SPEF2 transcript variant X2 XM_011514136.1:c.1301= XM_011514136.1:c.1301A>C
SPEF2 transcript variant 1 NM_024867.4:c.1301= NM_024867.4:c.1301A>C
SPEF2 transcript variant 1 NM_024867.3:c.1301= NM_024867.3:c.1301A>C
SPEF2 transcript variant 2 NM_144722.4:c.1301= NM_144722.4:c.1301A>C
SPEF2 transcript variant 2 NM_144722.3:c.1301= NM_144722.3:c.1301A>C
SPEF2 transcript variant X12 XR_925655.3:n.1436= XR_925655.3:n.1436A>C
SPEF2 transcript variant X12 XR_925655.2:n.1404= XR_925655.2:n.1404A>C
SPEF2 transcript variant X13 XR_925655.1:n.1517= XR_925655.1:n.1517A>C
SPEF2 transcript variant X6 XM_011514140.3:c.1130= XM_011514140.3:c.1130A>C
SPEF2 transcript variant X6 XM_011514140.2:c.1130= XM_011514140.2:c.1130A>C
SPEF2 transcript variant X6 XM_011514140.1:c.1130= XM_011514140.1:c.1130A>C
SPEF2 transcript variant X7 XM_017009880.3:c.1130= XM_017009880.3:c.1130A>C
SPEF2 transcript variant X7 XM_017009880.2:c.1130= XM_017009880.2:c.1130A>C
SPEF2 transcript variant X7 XM_017009880.1:c.1130= XM_017009880.1:c.1130A>C
SPEF2 transcript variant X16 XM_017009882.3:c.1301= XM_017009882.3:c.1301A>C
SPEF2 transcript variant X15 XM_017009882.2:c.1301= XM_017009882.2:c.1301A>C
SPEF2 transcript variant X16 XM_017009882.1:c.1301= XM_017009882.1:c.1301A>C
SPEF2 transcript variant X19 XM_024446219.2:c.1130= XM_024446219.2:c.1130A>C
SPEF2 transcript variant X17 XM_024446219.1:c.1130= XM_024446219.1:c.1130A>C
SPEF2 transcript variant X9 XM_047417766.1:c.875= XM_047417766.1:c.875A>C
SPEF2 transcript variant X8 XM_047417765.1:c.875= XM_047417765.1:c.875A>C
SPEF2 transcript variant X13 XM_047417767.1:c.1301= XM_047417767.1:c.1301A>C
SPEF2 transcript variant X14 XM_047417768.1:c.1301= XM_047417768.1:c.1301A>C
SPEF2 transcript variant X15 XM_047417769.1:c.1301= XM_047417769.1:c.1301A>C
SPEF2 transcript variant X18 XM_047417770.1:c.1301= XM_047417770.1:c.1301A>C
sperm flagellar protein 2 isoform X9 XP_005248433.1:p.Asp434= XP_005248433.1:p.Asp434Ala
sperm flagellar protein 2 isoform X10 XP_005248434.1:p.Asp434= XP_005248434.1:p.Asp434Ala
sperm flagellar protein 2 isoform X15 XP_005248435.1:p.Asp434= XP_005248435.1:p.Asp434Ala
sperm flagellar protein 2 isoform X1 XP_011512437.1:p.Asp434= XP_011512437.1:p.Asp434Ala
sperm flagellar protein 2 isoform X3 XP_011512439.1:p.Asp434= XP_011512439.1:p.Asp434Ala
sperm flagellar protein 2 isoform X4 XP_011512440.1:p.Asp434= XP_011512440.1:p.Asp434Ala
sperm flagellar protein 2 isoform X5 XP_011512441.1:p.Asp434= XP_011512441.1:p.Asp434Ala
sperm flagellar protein 2 isoform X2 XP_011512438.1:p.Asp434= XP_011512438.1:p.Asp434Ala
sperm flagellar protein 2 isoform 1 NP_079143.3:p.Asp434= NP_079143.3:p.Asp434Ala
sperm flagellar protein 2 isoform 2 NP_653323.1:p.Asp434= NP_653323.1:p.Asp434Ala
sperm flagellar protein 2 isoform X6 XP_011512442.1:p.Asp377= XP_011512442.1:p.Asp377Ala
sperm flagellar protein 2 isoform X7 XP_016865369.1:p.Asp377= XP_016865369.1:p.Asp377Ala
sperm flagellar protein 2 isoform X14 XP_016865371.1:p.Asp434= XP_016865371.1:p.Asp434Ala
sperm flagellar protein 2 isoform X17 XP_024301987.1:p.Asp377= XP_024301987.1:p.Asp377Ala
sperm flagellar protein 2 isoform X8 XP_047273722.1:p.Asp292= XP_047273722.1:p.Asp292Ala
sperm flagellar protein 2 isoform X8 XP_047273721.1:p.Asp292= XP_047273721.1:p.Asp292Ala
sperm flagellar protein 2 isoform X11 XP_047273723.1:p.Asp434= XP_047273723.1:p.Asp434Ala
sperm flagellar protein 2 isoform X12 XP_047273724.1:p.Asp434= XP_047273724.1:p.Asp434Ala
sperm flagellar protein 2 isoform X13 XP_047273725.1:p.Asp434= XP_047273725.1:p.Asp434Ala
sperm flagellar protein 2 isoform X16 XP_047273726.1:p.Asp434= XP_047273726.1:p.Asp434Ala
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 TOPMED ss4655834153 Apr 26, 2021 (155)
2 TopMed NC_000005.10 - 35667205 Apr 26, 2021 (155)
3 ALFA NC_000005.10 - 35667205 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
493211710, 12760277895, ss4655834153 NC_000005.10:35667204:A:C NC_000005.10:35667204:A:C (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 rs1481932653

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