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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs28942071

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr15:72345462 (GRCh38.p7) 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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00002 (5/246238, GnomAD)
A=0.00002 (3/125568, TOPMED)
A=0.00002 (2/121376, ExAC)
Clinical Significance
Reported in ClinVar
Gene : Consequence
HEXA : Missense Variant
Publications
10 citations
Genomic View
See rs on genome
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.p7 chr 15 NC_000015.10:g.72345462G>A
GRCh37.p13 chr 15 NC_000015.9:g.72637803G>A
HEXA RefSeqGene NG_009017.1:g.35718C>T
Gene: HEXA, hexosaminidase subunit alpha (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HEXA transcript variant 1 NM_001318825.1:c....

NM_001318825.1:c.1543C>T

R [CGC] > C [TGC] Coding Sequence Variant
beta-hexosaminidase subunit alpha isoform 1 precursor NP_001305754.1:p....

NP_001305754.1:p.Arg515Cys

R (Arg) > C (Cys) Missense Variant
HEXA transcript variant 2 NM_000520.5:c.151...

NM_000520.5:c.1510C>T

R [CGC] > C [TGC] Coding Sequence Variant
beta-hexosaminidase subunit alpha isoform 2 preproprotein NP_000511.2:p.Arg...

NP_000511.2:p.Arg504Cys

R (Arg) > C (Cys) Missense Variant
HEXA transcript variant 3 NR_134869.1:n.175...

NR_134869.1:n.1754C>T

N/A Non Coding Transcript Variant
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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: A (allele ID: 18945 )
ClinVar Accession Disease Names Clinical Significance
RCV000004112.2 Gm2-gangliosidosis, chronic Pathogenic
RCV000169084.1 Tay-Sachs disease Likely-Pathogenic
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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").

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Study Population Group Sample Size Ref Allele Alt Allele
Trans-Omics for Precision Medicine Global Study-wide 125568 G=0.99998 A=0.00002
The Exome Aggregation Consortium Global Study-wide 121376 G=0.99998 A=0.00002
The Exome Aggregation Consortium Europe Sub 73332 G=1.0000 A=0.0000
The Exome Aggregation Consortium Asian Sub 25160 G=1.0000 A=0.0000
The Exome Aggregation Consortium American Sub 11574 G=0.9999 A=0.0001
The Exome Aggregation Consortium African Sub 10402 G=1.0000 A=0.0000
The Exome Aggregation Consortium Other Sub 908 G=1.00 A=0.00
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= A Note
GRCh38.p7 chr 15 NC_000015.10:g.72345462G= NC_000015.10:g.72345462G>A
GRCh37.p13 chr 15 NC_000015.9:g.72637803G= NC_000015.9:g.72637803G>A
HEXA RefSeqGene NG_009017.1:g.35718C= NG_009017.1:g.35718C>T
HEXA transcript variant 2 NM_000520.5:c.1510C= NM_000520.5:c.1510C>T
HEXA transcript NM_000520.4:c.1510C= NM_000520.4:c.1510C>T
HEXA transcript variant 1 NM_001318825.1:c.1543C= NM_001318825.1:c.1543C>T
HEXA transcript variant 3 NR_134869.1:n.1754C= NR_134869.1:n.1754C>T
beta-hexosaminidase subunit alpha isoform 2 preproprotein NP_000511.2:p.Arg504= NP_000511.2:p.Arg504Cys
beta-hexosaminidase subunit alpha isoform 1 precursor NP_001305754.1:p.Arg515= NP_001305754.1:p.Arg515Cys
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#.

13 SubSNP, 2 ClinVar, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss262857279 Sep 17, 2010 (132)
2 NHLBI-ESP ss342407725 May 09, 2011 (134)
3 EVA_EXAC ss1691911613 Apr 01, 2015 (144)
4 ILLUMINA ss1946398021 Feb 12, 2016 (147)
5 ILLUMINA ss1959624867 Feb 12, 2016 (147)
6 HUMAN_LONGEVITY ss2208037033 Dec 20, 2016 (150)
7 TOPMED ss2372480879 Dec 20, 2016 (150)
8 GNOMAD ss2741376156 Nov 08, 2017 (151)
9 AFFY ss2985046178 Nov 08, 2017 (151)
10 ILLUMINA ss3021647740 Nov 08, 2017 (151)
11 TOPMED ss3231577174 Nov 08, 2017 (151)
12 ILLUMINA ss3625678157 Jul 20, 2018 (151)
13 ILLUMINA ss3644651137 Jul 20, 2018 (151)
14 The Exome Aggregation Consortium NC_000015.9 - 72637803 Jul 20, 2018 (151)
15 The Genome Aggregation Database NC_000015.9 - 72637803 Jul 20, 2018 (151)
16 Trans-Omics for Precision Medicine NC_000015.10 - 72345462 Jul 20, 2018 (151)
17 ClinVar RCV000004112.2 Jul 20, 2018 (151)
18 ClinVar RCV000169084.1 Jul 20, 2018 (151)
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
2291641, 10390891, ss342407725, ss1691911613, ss1946398021, ss1959624867, ss2372480879, ss2741376156, ss2985046178, ss3021647740, ss3625678157, ss3644651137 NC_000015.9:72637802:G= NC_000015.10:72345461:G= (self)
132727277, ss262857279, ss2208037033, ss3231577174 NC_000015.10:72345461:G= NC_000015.10:72345461:G= (self)
2291641, 10390891, ss342407725, ss1691911613, ss1946398021, ss1959624867, ss2372480879, ss2741376156, ss2985046178, ss3021647740, ss3625678157, ss3644651137 NC_000015.9:72637802:G>A NC_000015.10:72345461:G>A (self)
RCV000004112.2, RCV000169084.1, 132727277, ss262857279, ss2208037033, ss3231577174 NC_000015.10:72345461:G>A NC_000015.10:72345461:G>A (self)
Help

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

10 citations for rs28942071
PMID Title Author Year Journal
1827944 A third mutation at the CpG dinucleotide of codon 504 and a silent mutation at codon 506 of the HEX A gene. Paw BH et al. 1991 American journal of human genetics
1837283 Seven novel Tay-Sachs mutations detected by chemical mismatch cleavage of PCR-amplified cDNA fragments. Akli S et al. 1991 Genomics
2934978 GM2-ganglioside metabolism in hexosaminidase A deficiency states: determination in situ using labeled GM2 added to fibroblast cultures. Raghavan SS et al. 1985 American journal of human genetics
6236221 Faulty association of alpha- and beta-subunits in some forms of beta-hexosaminidase A deficiency. d'Azzo A et al. 1984 The Journal of biological chemistry
14577003 Structural basis of the GM2 gangliosidosis B variant. Matsuzawa F et al. 2003 Journal of human genetics
15714079 Late-onset Tay-Sachs disease: phenotypic characterization and genotypic correlations in 21 affected patients. Neudorfer O et al. 2005 Genetics in medicine
16088929 Molecular analysis of the HEXA gene in Italian patients with infantile and late onset Tay-Sachs disease: detection of fourteen novel alleles. Montalvo AL et al. 2005 Human mutation
18490185 Structural consequences of amino acid substitutions causing Tay-Sachs disease. Ohno K et al. 2008 Molecular genetics and metabolism
19091716 Late-onset Tay-Sachs disease presenting as a childhood stutter. Shapiro BE et al. 2009 Journal of neurology, neurosurgery, and psychiatry
22441121 Molecular analysis of HEXA gene in Argentinean patients affected with Tay-Sachs disease: possible common origin of the prevalent c.459+5A>G mutation. Zampieri S et al. 2012 Gene

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: 0.1.4.post833+d3ba21e