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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.

rs773351341

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr18:23545063 (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
A=0.000008 (1/121392, ExAC)
A=0.00000 (0/14528, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
NPC1 : 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 14528 C=1.00000 A=0.00000
European Sub 9690 C=1.0000 A=0.0000
African Sub 3324 C=1.0000 A=0.0000
African Others Sub 114 C=1.000 A=0.000
African American Sub 3210 C=1.0000 A=0.0000
Asian Sub 112 C=1.000 A=0.000
East Asian Sub 86 C=1.00 A=0.00
Other Asian Sub 26 C=1.00 A=0.00
Latin American 1 Sub 146 C=1.000 A=0.000
Latin American 2 Sub 610 C=1.000 A=0.000
South Asian Sub 98 C=1.00 A=0.00
Other Sub 548 C=1.000 A=0.000


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
ExAC Global Study-wide 121392 C=0.999992 A=0.000008
ExAC Europe Sub 73346 C=0.99999 A=0.00001
ExAC Asian Sub 25162 C=1.00000 A=0.00000
ExAC American Sub 11576 C=1.00000 A=0.00000
ExAC African Sub 10402 C=1.00000 A=0.00000
ExAC Other Sub 906 C=1.000 A=0.000
Allele Frequency Aggregator Total Global 14528 C=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 9690 C=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 3324 C=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 A=0.000
Allele Frequency Aggregator Other Sub 548 C=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 A=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 18 NC_000018.10:g.23545063C>A
GRCh38.p14 chr 18 NC_000018.10:g.23545063C>T
GRCh37.p13 chr 18 NC_000018.9:g.21125027C>A
GRCh37.p13 chr 18 NC_000018.9:g.21125027C>T
NPC1 RefSeqGene NG_012795.1:g.46555G>T
NPC1 RefSeqGene NG_012795.1:g.46555G>A
Gene: NPC1, NPC intracellular cholesterol transporter 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NPC1 transcript NM_000271.5:c.1844G>T R [CGT] > L [CTT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 precursor NP_000262.2:p.Arg615Leu R (Arg) > L (Leu) Missense Variant
NPC1 transcript NM_000271.5:c.1844G>A R [CGT] > H [CAT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 precursor NP_000262.2:p.Arg615His R (Arg) > H (His) Missense Variant
NPC1 transcript variant X1 XM_005258277.1:c.1895G>T R [CGT] > L [CTT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 isoform X1 XP_005258334.1:p.Arg632Leu R (Arg) > L (Leu) Missense Variant
NPC1 transcript variant X1 XM_005258277.1:c.1895G>A R [CGT] > H [CAT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 isoform X1 XP_005258334.1:p.Arg632His R (Arg) > H (His) Missense Variant
NPC1 transcript variant X4 XM_017025784.1:c.1895G>T R [CGT] > L [CTT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 isoform X4 XP_016881273.1:p.Arg632Leu R (Arg) > L (Leu) Missense Variant
NPC1 transcript variant X4 XM_017025784.1:c.1895G>A R [CGT] > H [CAT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 isoform X4 XP_016881273.1:p.Arg632His R (Arg) > H (His) Missense Variant
NPC1 transcript variant X6 XM_017025785.1:c.1895G>T R [CGT] > L [CTT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 isoform X6 XP_016881274.1:p.Arg632Leu R (Arg) > L (Leu) Missense Variant
NPC1 transcript variant X6 XM_017025785.1:c.1895G>A R [CGT] > H [CAT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 isoform X6 XP_016881274.1:p.Arg632His R (Arg) > H (His) Missense Variant
NPC1 transcript variant X2 XM_005258278.6:c.1895G>T R [CGT] > L [CTT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 isoform X2 XP_005258335.1:p.Arg632Leu R (Arg) > L (Leu) Missense Variant
NPC1 transcript variant X2 XM_005258278.6:c.1895G>A R [CGT] > H [CAT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 isoform X2 XP_005258335.1:p.Arg632His R (Arg) > H (His) Missense Variant
NPC1 transcript variant X3 XM_005258279.3:c.1844G>T R [CGT] > L [CTT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 isoform X3 XP_005258336.1:p.Arg615Leu R (Arg) > L (Leu) Missense Variant
NPC1 transcript variant X3 XM_005258279.3:c.1844G>A R [CGT] > H [CAT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 isoform X3 XP_005258336.1:p.Arg615His R (Arg) > H (His) Missense Variant
NPC1 transcript variant X5 XM_006722479.4:c.1895G>T R [CGT] > L [CTT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 isoform X5 XP_006722542.1:p.Arg632Leu R (Arg) > L (Leu) Missense Variant
NPC1 transcript variant X5 XM_006722479.4:c.1895G>A R [CGT] > H [CAT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 isoform X5 XP_006722542.1:p.Arg632His R (Arg) > H (His) Missense Variant
NPC1 transcript variant X7 XM_017025786.2:c.1844G>T R [CGT] > L [CTT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 isoform X7 XP_016881275.1:p.Arg615Leu R (Arg) > L (Leu) Missense Variant
NPC1 transcript variant X7 XM_017025786.2:c.1844G>A R [CGT] > H [CAT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 isoform X7 XP_016881275.1:p.Arg615His R (Arg) > H (His) Missense Variant
NPC1 transcript variant X8 XM_017025787.2:c.1844G>T R [CGT] > L [CTT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 isoform X8 XP_016881276.1:p.Arg615Leu R (Arg) > L (Leu) Missense Variant
NPC1 transcript variant X8 XM_017025787.2:c.1844G>A R [CGT] > H [CAT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 isoform X8 XP_016881276.1:p.Arg615His R (Arg) > H (His) Missense Variant
NPC1 transcript variant X9 XM_047437539.1:c.1844G>T R [CGT] > L [CTT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 isoform X9 XP_047293495.1:p.Arg615Leu R (Arg) > L (Leu) Missense Variant
NPC1 transcript variant X9 XM_047437539.1:c.1844G>A R [CGT] > H [CAT] Coding Sequence Variant
NPC intracellular cholesterol transporter 1 isoform X9 XP_047293495.1:p.Arg615His R (Arg) > H (His) Missense 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: 1342533 )
ClinVar Accession Disease Names Clinical Significance
RCV001988681.1 Niemann-Pick disease, type C1 Likely-Pathogenic
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 18 NC_000018.10:g.23545063= NC_000018.10:g.23545063C>A NC_000018.10:g.23545063C>T
GRCh37.p13 chr 18 NC_000018.9:g.21125027= NC_000018.9:g.21125027C>A NC_000018.9:g.21125027C>T
NPC1 RefSeqGene NG_012795.1:g.46555= NG_012795.1:g.46555G>T NG_012795.1:g.46555G>A
NPC1 transcript NM_000271.5:c.1844= NM_000271.5:c.1844G>T NM_000271.5:c.1844G>A
NPC1 transcript NM_000271.4:c.1844= NM_000271.4:c.1844G>T NM_000271.4:c.1844G>A
NPC1 transcript variant X2 XM_005258278.6:c.1895= XM_005258278.6:c.1895G>T XM_005258278.6:c.1895G>A
NPC1 transcript variant X2 XM_005258278.5:c.1895= XM_005258278.5:c.1895G>T XM_005258278.5:c.1895G>A
NPC1 transcript variant X2 XM_005258278.4:c.1895= XM_005258278.4:c.1895G>T XM_005258278.4:c.1895G>A
NPC1 transcript variant X2 XM_005258278.3:c.1895= XM_005258278.3:c.1895G>T XM_005258278.3:c.1895G>A
NPC1 transcript variant X2 XM_005258278.2:c.1895= XM_005258278.2:c.1895G>T XM_005258278.2:c.1895G>A
NPC1 transcript variant X2 XM_005258278.1:c.1895= XM_005258278.1:c.1895G>T XM_005258278.1:c.1895G>A
NPC1 transcript variant X5 XM_006722479.4:c.1895= XM_006722479.4:c.1895G>T XM_006722479.4:c.1895G>A
NPC1 transcript variant X5 XM_006722479.3:c.1895= XM_006722479.3:c.1895G>T XM_006722479.3:c.1895G>A
NPC1 transcript variant X4 XM_006722479.2:c.1895= XM_006722479.2:c.1895G>T XM_006722479.2:c.1895G>A
NPC1 transcript variant X4 XM_006722479.1:c.1895= XM_006722479.1:c.1895G>T XM_006722479.1:c.1895G>A
NPC1 transcript variant X3 XM_005258279.3:c.1844= XM_005258279.3:c.1844G>T XM_005258279.3:c.1844G>A
NPC1 transcript variant X3 XM_005258279.2:c.1844= XM_005258279.2:c.1844G>T XM_005258279.2:c.1844G>A
NPC1 transcript variant X3 XM_005258279.1:c.1844= XM_005258279.1:c.1844G>T XM_005258279.1:c.1844G>A
NPC1 transcript variant X7 XM_017025786.2:c.1844= XM_017025786.2:c.1844G>T XM_017025786.2:c.1844G>A
NPC1 transcript variant X7 XM_017025786.1:c.1844= XM_017025786.1:c.1844G>T XM_017025786.1:c.1844G>A
NPC1 transcript variant X8 XM_017025787.2:c.1844= XM_017025787.2:c.1844G>T XM_017025787.2:c.1844G>A
NPC1 transcript variant X8 XM_017025787.1:c.1844= XM_017025787.1:c.1844G>T XM_017025787.1:c.1844G>A
NPC1 transcript variant X4 XM_017025784.1:c.1895= XM_017025784.1:c.1895G>T XM_017025784.1:c.1895G>A
NPC1 transcript variant X6 XM_017025785.1:c.1895= XM_017025785.1:c.1895G>T XM_017025785.1:c.1895G>A
NPC1 transcript variant X9 XM_047437539.1:c.1844= XM_047437539.1:c.1844G>T XM_047437539.1:c.1844G>A
NPC1 transcript variant X1 XM_005258277.1:c.1895= XM_005258277.1:c.1895G>T XM_005258277.1:c.1895G>A
NPC intracellular cholesterol transporter 1 precursor NP_000262.2:p.Arg615= NP_000262.2:p.Arg615Leu NP_000262.2:p.Arg615His
NPC intracellular cholesterol transporter 1 isoform X2 XP_005258335.1:p.Arg632= XP_005258335.1:p.Arg632Leu XP_005258335.1:p.Arg632His
NPC intracellular cholesterol transporter 1 isoform X5 XP_006722542.1:p.Arg632= XP_006722542.1:p.Arg632Leu XP_006722542.1:p.Arg632His
NPC intracellular cholesterol transporter 1 isoform X3 XP_005258336.1:p.Arg615= XP_005258336.1:p.Arg615Leu XP_005258336.1:p.Arg615His
NPC intracellular cholesterol transporter 1 isoform X7 XP_016881275.1:p.Arg615= XP_016881275.1:p.Arg615Leu XP_016881275.1:p.Arg615His
NPC intracellular cholesterol transporter 1 isoform X8 XP_016881276.1:p.Arg615= XP_016881276.1:p.Arg615Leu XP_016881276.1:p.Arg615His
NPC intracellular cholesterol transporter 1 isoform X4 XP_016881273.1:p.Arg632= XP_016881273.1:p.Arg632Leu XP_016881273.1:p.Arg632His
NPC intracellular cholesterol transporter 1 isoform X6 XP_016881274.1:p.Arg632= XP_016881274.1:p.Arg632Leu XP_016881274.1:p.Arg632His
NPC intracellular cholesterol transporter 1 isoform X9 XP_047293495.1:p.Arg615= XP_047293495.1:p.Arg615Leu XP_047293495.1:p.Arg615His
NPC intracellular cholesterol transporter 1 isoform X1 XP_005258334.1:p.Arg632= XP_005258334.1:p.Arg632Leu XP_005258334.1:p.Arg632His
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, 4 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1693103714 Apr 01, 2015 (144)
2 GNOMAD ss2743224906 Nov 08, 2017 (151)
3 ILLUMINA ss3021829320 Nov 08, 2017 (151)
4 ILLUMINA ss3652249602 Oct 12, 2018 (152)
5 ILLUMINA ss3725663750 Jul 13, 2019 (153)
6 ExAC NC_000018.9 - 21125027 Oct 12, 2018 (152)
7 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 12535177 (NC_000018.9:21125026:C:C 251475/251476, NC_000018.9:21125026:C:A 1/251476)
Row 12535178 (NC_000018.9:21125026:C:C 251475/251476, NC_000018.9:21125026:C:T 1/251476)

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

Submission ignored due to conflicting rows:
Row 12535177 (NC_000018.9:21125026:C:C 251475/251476, NC_000018.9:21125026:C:A 1/251476)
Row 12535178 (NC_000018.9:21125026:C:C 251475/251476, NC_000018.9:21125026:C:T 1/251476)

- Jul 13, 2019 (153)
9 ALFA NC_000018.10 - 23545063 Apr 27, 2021 (155)
10 ClinVar RCV001988681.1 Oct 16, 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
3571888, ss1693103714, ss2743224906, ss3021829320, ss3652249602 NC_000018.9:21125026:C:A NC_000018.10:23545062:C:A (self)
8971515629, ss3725663750 NC_000018.10:23545062:C:A NC_000018.10:23545062:C:A (self)
ss2743224906 NC_000018.9:21125026:C:T NC_000018.10:23545062:C:T (self)
RCV001988681.1 NC_000018.10:23545062:C:T NC_000018.10:23545062:C:T
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 rs773351341

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