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dbSNP Short Genetic Variations

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.

rs776979024

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr16:3608803 (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
G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000011 (3/264690, TOPMED)
T=0.000020 (5/251492, GnomAD_exome)
T=0.000036 (5/140194, GnomAD) (+ 2 more)
T=0.000008 (1/121410, ExAC)
T=0.00008 (3/35432, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
SLX4 : Synonymous 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 51794 G=0.99992 T=0.00008
European Sub 36678 G=0.99995 T=0.00005
African Sub 7756 G=0.9999 T=0.0001
African Others Sub 298 G=1.000 T=0.000
African American Sub 7458 G=0.9999 T=0.0001
Asian Sub 112 G=1.000 T=0.000
East Asian Sub 86 G=1.00 T=0.00
Other Asian Sub 26 G=1.00 T=0.00
Latin American 1 Sub 500 G=1.000 T=0.000
Latin American 2 Sub 628 G=1.000 T=0.000
South Asian Sub 98 G=1.00 T=0.00
Other Sub 6022 G=0.9998 T=0.0002


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 G=0.999989 T=0.000011
gnomAD - Exomes Global Study-wide 251492 G=0.999980 T=0.000020
gnomAD - Exomes European Sub 135416 G=0.999963 T=0.000037
gnomAD - Exomes Asian Sub 49010 G=1.00000 T=0.00000
gnomAD - Exomes American Sub 34592 G=1.00000 T=0.00000
gnomAD - Exomes African Sub 16256 G=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10080 G=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6138 G=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140194 G=0.999964 T=0.000036
gnomAD - Genomes European Sub 75942 G=0.99996 T=0.00004
gnomAD - Genomes African Sub 41996 G=0.99998 T=0.00002
gnomAD - Genomes American Sub 13648 G=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2152 G=0.9995 T=0.0005
ExAC Global Study-wide 121410 G=0.999992 T=0.000008
ExAC Europe Sub 73354 G=0.99999 T=0.00001
ExAC Asian Sub 25166 G=1.00000 T=0.00000
ExAC American Sub 11578 G=1.00000 T=0.00000
ExAC African Sub 10406 G=1.00000 T=0.00000
ExAC Other Sub 906 G=1.000 T=0.000
Allele Frequency Aggregator Total Global 35432 G=0.99992 T=0.00008
Allele Frequency Aggregator European Sub 26588 G=0.99992 T=0.00008
Allele Frequency Aggregator Other Sub 4588 G=0.9998 T=0.0002
Allele Frequency Aggregator African Sub 2918 G=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 G=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 G=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 T=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 16 NC_000016.10:g.3608803G>T
GRCh37.p13 chr 16 NC_000016.9:g.3658804G>T
SLX4 RefSeqGene (LRG_503) NG_028123.1:g.7782C>A
Gene: SLX4, SLX4 structure-specific endonuclease subunit (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLX4 transcript NM_032444.4:c.162C>A L [CTC] > L [CTA] Coding Sequence Variant
structure-specific endonuclease subunit SLX4 NP_115820.2:p.Leu54= L (Leu) > L (Leu) Synonymous Variant
SLX4 transcript variant X4 XM_047434801.1:c. N/A Genic Upstream Transcript Variant
SLX4 transcript variant X1 XM_024450471.2:c.162C>A L [CTC] > L [CTA] Coding Sequence Variant
structure-specific endonuclease subunit SLX4 isoform X1 XP_024306239.1:p.Leu54= L (Leu) > L (Leu) Synonymous Variant
SLX4 transcript variant X2 XM_011522715.4:c.162C>A L [CTC] > L [CTA] Coding Sequence Variant
structure-specific endonuclease subunit SLX4 isoform X2 XP_011521017.1:p.Leu54= L (Leu) > L (Leu) Synonymous Variant
SLX4 transcript variant X3 XR_007064923.1:n.811C>A 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.

Allele: T (allele ID: 1082039 )
ClinVar Accession Disease Names Clinical Significance
RCV001395721.5 Fanconi anemia Likely-Benign
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 G= T
GRCh38.p14 chr 16 NC_000016.10:g.3608803= NC_000016.10:g.3608803G>T
GRCh37.p13 chr 16 NC_000016.9:g.3658804= NC_000016.9:g.3658804G>T
SLX4 RefSeqGene (LRG_503) NG_028123.1:g.7782= NG_028123.1:g.7782C>A
SLX4 transcript NM_032444.4:c.162= NM_032444.4:c.162C>A
SLX4 transcript NM_032444.3:c.162= NM_032444.3:c.162C>A
SLX4 transcript NM_032444.2:c.162= NM_032444.2:c.162C>A
SLX4 transcript variant X2 XM_011522715.4:c.162= XM_011522715.4:c.162C>A
SLX4 transcript variant X2 XM_011522715.3:c.162= XM_011522715.3:c.162C>A
SLX4 transcript variant X1 XM_011522715.2:c.162= XM_011522715.2:c.162C>A
SLX4 transcript variant X1 XM_011522715.1:c.162= XM_011522715.1:c.162C>A
SLX4 transcript variant X1 XM_024450471.2:c.162= XM_024450471.2:c.162C>A
SLX4 transcript variant X1 XM_024450471.1:c.162= XM_024450471.1:c.162C>A
SLX4 transcript variant X3 XR_007064923.1:n.811= XR_007064923.1:n.811C>A
structure-specific endonuclease subunit SLX4 NP_115820.2:p.Leu54= NP_115820.2:p.Leu54=
structure-specific endonuclease subunit SLX4 isoform X2 XP_011521017.1:p.Leu54= XP_011521017.1:p.Leu54=
structure-specific endonuclease subunit SLX4 isoform X1 XP_024306239.1:p.Leu54= XP_024306239.1:p.Leu54=
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#.

5 SubSNP, 5 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1692122883 Apr 01, 2015 (144)
2 GNOMAD ss2741702394 Nov 08, 2017 (151)
3 GNOMAD ss2749451045 Nov 08, 2017 (151)
4 GNOMAD ss2939521716 Nov 08, 2017 (151)
5 TOPMED ss5005361561 Apr 26, 2021 (155)
6 ExAC NC_000016.9 - 3658804 Oct 12, 2018 (152)
7 gnomAD - Genomes NC_000016.10 - 3608803 Apr 26, 2021 (155)
8 gnomAD - Exomes NC_000016.9 - 3658804 Jul 13, 2019 (153)
9 TopMed NC_000016.10 - 3608803 Apr 26, 2021 (155)
10 ALFA NC_000016.10 - 3608803 Apr 26, 2021 (155)
11 ClinVar RCV001395721.5 Oct 17, 2022 (156)
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
2517376, 10976950, ss1692122883, ss2741702394, ss2749451045, ss2939521716 NC_000016.9:3658803:G:T NC_000016.10:3608802:G:T (self)
RCV001395721.5, 480798341, 220907222, 6709703513, ss5005361561 NC_000016.10:3608802:G:T NC_000016.10:3608802:G: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 rs776979024

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.post761+d5e8e07