Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs1457090032

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr14:77708131 (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>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000011 (3/264690, TOPMED)
T=0.000004 (1/251370, GnomAD_exome)
T=0.000014 (2/140262, GnomAD) (+ 3 more)
T=0.00004 (1/28258, 14KJPN)
C=0.00000 (0/11862, ALFA)
T=0.00000 (0/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLIRP : Missense Variant
ALKBH1 : 2KB Upstream 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 11862 G=1.00000 C=0.00000, T=0.00000 1.0 0.0 0.0 N/A
European Sub 7618 G=1.0000 C=0.0000, T=0.0000 1.0 0.0 0.0 N/A
African Sub 2816 G=1.0000 C=0.0000, T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 G=1.000 C=0.000, T=0.000 1.0 0.0 0.0 N/A
African American Sub 2708 G=1.0000 C=0.0000, T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 G=1.000 C=0.000, T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 G=1.00 C=0.00, T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 G=1.00 C=0.00, T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 G=1.000 C=0.000, T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 G=1.000 C=0.000, T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 G=1.00 C=0.00, T=0.00 1.0 0.0 0.0 N/A
Other Sub 470 G=1.000 C=0.000, T=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
TopMed Global Study-wide 264690 G=0.999989 T=0.000011
gnomAD - Exomes Global Study-wide 251370 G=0.999996 T=0.000004
gnomAD - Exomes European Sub 135314 G=0.999993 T=0.000007
gnomAD - Exomes Asian Sub 49006 G=1.00000 T=0.00000
gnomAD - Exomes American Sub 34588 G=1.00000 T=0.00000
gnomAD - Exomes African Sub 16252 G=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10074 G=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6136 G=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140262 G=0.999986 T=0.000014
gnomAD - Genomes European Sub 75962 G=0.99997 T=0.00003
gnomAD - Genomes African Sub 42034 G=1.00000 T=0.00000
gnomAD - Genomes American Sub 13658 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=1.0000 T=0.0000
14KJPN JAPANESE Study-wide 28258 G=0.99996 T=0.00004
Allele Frequency Aggregator Total Global 11862 G=1.00000 C=0.00000, T=0.00000
Allele Frequency Aggregator European Sub 7618 G=1.0000 C=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 2816 G=1.0000 C=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 C=0.000, T=0.000
Allele Frequency Aggregator Other Sub 470 G=1.000 C=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 C=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 108 G=1.000 C=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 94 G=1.00 C=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 14 NC_000014.9:g.77708131G>C
GRCh38.p14 chr 14 NC_000014.9:g.77708131G>T
GRCh37.p13 chr 14 NC_000014.8:g.78174474G>C
GRCh37.p13 chr 14 NC_000014.8:g.78174474G>T
Gene: ALKBH1, alkB homolog 1, histone H2A dioxygenase (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
ALKBH1 transcript NM_006020.3:c. N/A Upstream Transcript Variant
ALKBH1 transcript variant X1 XM_047431848.1:c. N/A Upstream Transcript Variant
Gene: SLIRP, SRA stem-loop interacting RNA binding protein (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SLIRP transcript variant 2 NM_001267863.1:c.20G>C R [AGA] > T [ACA] Coding Sequence Variant
SRA stem-loop-interacting RNA-binding protein, mitochondrial isoform 2 precursor NP_001254792.1:p.Arg7Thr R (Arg) > T (Thr) Missense Variant
SLIRP transcript variant 2 NM_001267863.1:c.20G>T R [AGA] > I [ATA] Coding Sequence Variant
SRA stem-loop-interacting RNA-binding protein, mitochondrial isoform 2 precursor NP_001254792.1:p.Arg7Ile R (Arg) > I (Ile) Missense Variant
SLIRP transcript variant 3 NM_001267864.1:c.20G>C R [AGA] > T [ACA] Coding Sequence Variant
SRA stem-loop-interacting RNA-binding protein, mitochondrial isoform 3 precursor NP_001254793.1:p.Arg7Thr R (Arg) > T (Thr) Missense Variant
SLIRP transcript variant 3 NM_001267864.1:c.20G>T R [AGA] > I [ATA] Coding Sequence Variant
SRA stem-loop-interacting RNA-binding protein, mitochondrial isoform 3 precursor NP_001254793.1:p.Arg7Ile R (Arg) > I (Ile) Missense Variant
SLIRP transcript variant 1 NM_031210.6:c.20G>C R [AGA] > T [ACA] Coding Sequence Variant
SRA stem-loop-interacting RNA-binding protein, mitochondrial isoform 1 precursor NP_112487.1:p.Arg7Thr R (Arg) > T (Thr) Missense Variant
SLIRP transcript variant 1 NM_031210.6:c.20G>T R [AGA] > I [ATA] Coding Sequence Variant
SRA stem-loop-interacting RNA-binding protein, mitochondrial isoform 1 precursor NP_112487.1:p.Arg7Ile R (Arg) > I (Ile) Missense Variant
SLIRP transcript variant 4 NR_052025.2:n.29G>C N/A Non Coding Transcript Variant
SLIRP transcript variant 4 NR_052025.2:n.29G>T 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 G= C T
GRCh38.p14 chr 14 NC_000014.9:g.77708131= NC_000014.9:g.77708131G>C NC_000014.9:g.77708131G>T
GRCh37.p13 chr 14 NC_000014.8:g.78174474= NC_000014.8:g.78174474G>C NC_000014.8:g.78174474G>T
SLIRP transcript variant 1 NM_031210.6:c.20= NM_031210.6:c.20G>C NM_031210.6:c.20G>T
SLIRP transcript variant 1 NM_031210.5:c.20= NM_031210.5:c.20G>C NM_031210.5:c.20G>T
SLIRP transcript variant 4 NR_052025.2:n.29= NR_052025.2:n.29G>C NR_052025.2:n.29G>T
SLIRP transcript variant 4 NR_052025.1:n.61= NR_052025.1:n.61G>C NR_052025.1:n.61G>T
SLIRP transcript variant 3 NM_001267864.1:c.20= NM_001267864.1:c.20G>C NM_001267864.1:c.20G>T
SLIRP transcript variant 2 NM_001267863.1:c.20= NM_001267863.1:c.20G>C NM_001267863.1:c.20G>T
SRA stem-loop-interacting RNA-binding protein, mitochondrial isoform 1 precursor NP_112487.1:p.Arg7= NP_112487.1:p.Arg7Thr NP_112487.1:p.Arg7Ile
SRA stem-loop-interacting RNA-binding protein, mitochondrial isoform 3 precursor NP_001254793.1:p.Arg7= NP_001254793.1:p.Arg7Thr NP_001254793.1:p.Arg7Ile
SRA stem-loop-interacting RNA-binding protein, mitochondrial isoform 2 precursor NP_001254792.1:p.Arg7= NP_001254792.1:p.Arg7Thr NP_001254792.1:p.Arg7Ile
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#.

4 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2740864061 Nov 08, 2017 (151)
2 GNOMAD ss4281184368 Apr 27, 2021 (155)
3 TOPMED ss4976895388 Apr 27, 2021 (155)
4 TOMMO_GENOMICS ss5767103619 Oct 16, 2022 (156)
5 gnomAD - Genomes NC_000014.9 - 77708131 Apr 27, 2021 (155)
6 gnomAD - Exomes NC_000014.8 - 78174474 Jul 13, 2019 (153)
7 14KJPN NC_000014.9 - 77708131 Oct 16, 2022 (156)
8 TopMed NC_000014.9 - 77708131 Apr 27, 2021 (155)
9 ALFA NC_000014.9 - 77708131 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
5013165766 NC_000014.9:77708130:G:C NC_000014.9:77708130:G:C (self)
10120385, ss2740864061 NC_000014.8:78174473:G:T NC_000014.9:77708130:G:T (self)
456429432, 100940723, 192441047, 5013165766, ss4281184368, ss4976895388, ss5767103619 NC_000014.9:77708130:G:T NC_000014.9:77708130: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 rs1457090032

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