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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.

rs1486711258

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:28490390 (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>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00003 (1/35428, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC13A2 : 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 35428 C=0.99997 A=0.00000, T=0.00003 0.999944 0.0 5.6e-05 0
European Sub 26586 C=0.99996 A=0.00000, T=0.00004 0.999925 0.0 0.000075 0
African Sub 2918 C=1.0000 A=0.0000, T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 C=1.000 A=0.000, T=0.000 1.0 0.0 0.0 N/A
African American Sub 2804 C=1.0000 A=0.0000, T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 C=1.000 A=0.000, T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 C=1.00 A=0.00, T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 C=1.00 A=0.00, T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 500 C=1.000 A=0.000, T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 628 C=1.000 A=0.000, T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 C=1.00 A=0.00, T=0.00 1.0 0.0 0.0 N/A
Other Sub 4586 C=1.0000 A=0.0000, 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
Allele Frequency Aggregator Total Global 35428 C=0.99997 A=0.00000, T=0.00003
Allele Frequency Aggregator European Sub 26586 C=0.99996 A=0.00000, T=0.00004
Allele Frequency Aggregator Other Sub 4586 C=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 2918 C=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 A=0.00, 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 17 NC_000017.11:g.28490390C>A
GRCh38.p14 chr 17 NC_000017.11:g.28490390C>T
GRCh37.p13 chr 17 NC_000017.10:g.26817408C>A
GRCh37.p13 chr 17 NC_000017.10:g.26817408C>T
SLC13A2 RefSeqGene NG_051960.1:g.21745C>A
SLC13A2 RefSeqGene NG_051960.1:g.21745C>T
GRCh37.p13 chr 17 fix patch HG883_PATCH NW_003871090.1:g.172251C>A
GRCh37.p13 chr 17 fix patch HG883_PATCH NW_003871090.1:g.172251C>T
Gene: SLC13A2, solute carrier family 13 member 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC13A2 transcript variant 4 NM_001346683.2:c.100-64C>A N/A Intron Variant
SLC13A2 transcript variant 5 NM_001346684.2:c.18+22C>A N/A Intron Variant
SLC13A2 transcript variant 2 NM_003984.4:c.232-64C>A N/A Intron Variant
SLC13A2 transcript variant 1 NM_001145975.2:c.315C>A N [AAC] > K [AAA] Coding Sequence Variant
solute carrier family 13 member 2 isoform a NP_001139447.1:p.Asn105Lys N (Asn) > K (Lys) Missense Variant
SLC13A2 transcript variant 1 NM_001145975.2:c.315C>T N [AAC] > N [AAT] Coding Sequence Variant
solute carrier family 13 member 2 isoform a NP_001139447.1:p.Asn105= N (Asn) > N (Asn) Synonymous Variant
SLC13A2 transcript variant X3 XM_011525452.2:c.232-64C>A N/A Intron Variant
SLC13A2 transcript variant X1 XM_011525450.4:c.315C>A N [AAC] > K [AAA] Coding Sequence Variant
solute carrier family 13 member 2 isoform X1 XP_011523752.1:p.Asn105Lys N (Asn) > K (Lys) Missense Variant
SLC13A2 transcript variant X1 XM_011525450.4:c.315C>T N [AAC] > N [AAT] Coding Sequence Variant
solute carrier family 13 member 2 isoform X1 XP_011523752.1:p.Asn105= N (Asn) > N (Asn) Synonymous Variant
SLC13A2 transcript variant X2 XM_047437011.1:c.183C>A N [AAC] > K [AAA] Coding Sequence Variant
solute carrier family 13 member 2 isoform X2 XP_047292967.1:p.Asn61Lys N (Asn) > K (Lys) Missense Variant
SLC13A2 transcript variant X2 XM_047437011.1:c.183C>T N [AAC] > N [AAT] Coding Sequence Variant
solute carrier family 13 member 2 isoform X2 XP_047292967.1:p.Asn61= N (Asn) > N (Asn) Synonymous Variant
SLC13A2 transcript variant X4 XM_011525453.3:c.315C>A N [AAC] > K [AAA] Coding Sequence Variant
solute carrier family 13 member 2 isoform X4 XP_011523755.1:p.Asn105Lys N (Asn) > K (Lys) Missense Variant
SLC13A2 transcript variant X4 XM_011525453.3:c.315C>T N [AAC] > N [AAT] Coding Sequence Variant
solute carrier family 13 member 2 isoform X4 XP_011523755.1:p.Asn105= N (Asn) > N (Asn) Synonymous Variant
SLC13A2 transcript variant X5 XM_011525454.4:c.315C>A N [AAC] > K [AAA] Coding Sequence Variant
solute carrier family 13 member 2 isoform X5 XP_011523756.1:p.Asn105Lys N (Asn) > K (Lys) Missense Variant
SLC13A2 transcript variant X5 XM_011525454.4:c.315C>T N [AAC] > N [AAT] Coding Sequence Variant
solute carrier family 13 member 2 isoform X5 XP_011523756.1:p.Asn105= N (Asn) > N (Asn) Synonymous 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= A T
GRCh38.p14 chr 17 NC_000017.11:g.28490390= NC_000017.11:g.28490390C>A NC_000017.11:g.28490390C>T
GRCh37.p13 chr 17 NC_000017.10:g.26817408= NC_000017.10:g.26817408C>A NC_000017.10:g.26817408C>T
SLC13A2 RefSeqGene NG_051960.1:g.21745= NG_051960.1:g.21745C>A NG_051960.1:g.21745C>T
SLC13A2 transcript variant 1 NM_001145975.2:c.315= NM_001145975.2:c.315C>A NM_001145975.2:c.315C>T
SLC13A2 transcript variant 1 NM_001145975.1:c.315= NM_001145975.1:c.315C>A NM_001145975.1:c.315C>T
GRCh37.p13 chr 17 fix patch HG883_PATCH NW_003871090.1:g.172251= NW_003871090.1:g.172251C>A NW_003871090.1:g.172251C>T
SLC13A2 transcript variant X1 XM_011525450.4:c.315= XM_011525450.4:c.315C>A XM_011525450.4:c.315C>T
SLC13A2 transcript variant X1 XM_011525450.3:c.315= XM_011525450.3:c.315C>A XM_011525450.3:c.315C>T
SLC13A2 transcript variant X1 XM_011525450.2:c.315= XM_011525450.2:c.315C>A XM_011525450.2:c.315C>T
SLC13A2 transcript variant X1 XM_011525450.1:c.315= XM_011525450.1:c.315C>A XM_011525450.1:c.315C>T
SLC13A2 transcript variant X5 XM_011525454.4:c.315= XM_011525454.4:c.315C>A XM_011525454.4:c.315C>T
SLC13A2 transcript variant X6 XM_011525454.3:c.315= XM_011525454.3:c.315C>A XM_011525454.3:c.315C>T
SLC13A2 transcript variant X6 XM_011525454.2:c.315= XM_011525454.2:c.315C>A XM_011525454.2:c.315C>T
SLC13A2 transcript variant X6 XM_011525454.1:c.315= XM_011525454.1:c.315C>A XM_011525454.1:c.315C>T
SLC13A2 transcript variant X4 XM_011525453.3:c.315= XM_011525453.3:c.315C>A XM_011525453.3:c.315C>T
SLC13A2 transcript variant X4 XM_011525453.2:c.315= XM_011525453.2:c.315C>A XM_011525453.2:c.315C>T
SLC13A2 transcript variant X4 XM_011525453.1:c.315= XM_011525453.1:c.315C>A XM_011525453.1:c.315C>T
SLC13A2 transcript variant X2 XM_047437011.1:c.183= XM_047437011.1:c.183C>A XM_047437011.1:c.183C>T
solute carrier family 13 member 2 isoform a NP_001139447.1:p.Asn105= NP_001139447.1:p.Asn105Lys NP_001139447.1:p.Asn105=
solute carrier family 13 member 2 isoform X1 XP_011523752.1:p.Asn105= XP_011523752.1:p.Asn105Lys XP_011523752.1:p.Asn105=
solute carrier family 13 member 2 isoform X5 XP_011523756.1:p.Asn105= XP_011523756.1:p.Asn105Lys XP_011523756.1:p.Asn105=
solute carrier family 13 member 2 isoform X4 XP_011523755.1:p.Asn105= XP_011523755.1:p.Asn105Lys XP_011523755.1:p.Asn105=
solute carrier family 13 member 2 isoform X2 XP_047292967.1:p.Asn61= XP_047292967.1:p.Asn61Lys XP_047292967.1:p.Asn61=
SLC13A2 transcript variant 4 NM_001346683.2:c.100-64= NM_001346683.2:c.100-64C>A NM_001346683.2:c.100-64C>T
SLC13A2 transcript variant 5 NM_001346684.2:c.18+22= NM_001346684.2:c.18+22C>A NM_001346684.2:c.18+22C>T
SLC13A2 transcript variant 2 NM_003984.3:c.232-64= NM_003984.3:c.232-64C>A NM_003984.3:c.232-64C>T
SLC13A2 transcript variant 2 NM_003984.4:c.232-64= NM_003984.4:c.232-64C>A NM_003984.4:c.232-64C>T
SLC13A2 transcript variant X3 XM_011525452.2:c.232-64= XM_011525452.2:c.232-64C>A XM_011525452.2:c.232-64C>T
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, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2742560069 Oct 12, 2018 (152)
2 GNOMAD ss4309877870 Apr 27, 2021 (155)
3 GNOMAD ss4309877871 Apr 27, 2021 (155)
4 TOPMED ss5032707018 Apr 27, 2021 (155)
5 TOPMED ss5032707019 Apr 27, 2021 (155)
6 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 504454407 (NC_000017.11:28490389:C:A 1/140242)
Row 504454408 (NC_000017.11:28490389:C:T 1/140242)

- Apr 27, 2021 (155)
7 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 504454407 (NC_000017.11:28490389:C:A 1/140242)
Row 504454408 (NC_000017.11:28490389:C:T 1/140242)

- Apr 27, 2021 (155)
8 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 11861940 (NC_000017.10:26817407:C:C 251231/251232, NC_000017.10:26817407:C:A 1/251232)
Row 11861941 (NC_000017.10:26817407:C:C 251230/251232, NC_000017.10:26817407:C:T 2/251232)

- Jul 13, 2019 (153)
9 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 11861940 (NC_000017.10:26817407:C:C 251231/251232, NC_000017.10:26817407:C:A 1/251232)
Row 11861941 (NC_000017.10:26817407:C:C 251230/251232, NC_000017.10:26817407:C:T 2/251232)

- Jul 13, 2019 (153)
10 TopMed

Submission ignored due to conflicting rows:
Row 248252680 (NC_000017.11:28490389:C:A 1/264690)
Row 248252681 (NC_000017.11:28490389:C:T 2/264690)

- Apr 27, 2021 (155)
11 TopMed

Submission ignored due to conflicting rows:
Row 248252680 (NC_000017.11:28490389:C:A 1/264690)
Row 248252681 (NC_000017.11:28490389:C:T 2/264690)

- Apr 27, 2021 (155)
12 ALFA NC_000017.11 - 28490390 Apr 27, 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
ss2742560069 NC_000017.10:26817407:C:A NC_000017.11:28490389:C:A (self)
14653615364, ss4309877870, ss5032707018 NC_000017.11:28490389:C:A NC_000017.11:28490389:C:A (self)
ss2742560069 NC_000017.10:26817407:C:T NC_000017.11:28490389:C:T (self)
14653615364, ss4309877871, ss5032707019 NC_000017.11:28490389:C:T NC_000017.11:28490389: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 rs1486711258

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