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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.

rs541202772

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:225406664 (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>A / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000036 (9/247992, GnomAD_exome)
T=0.000007 (1/140148, GnomAD)
A=0.000050 (6/120576, ExAC) (+ 5 more)
A=0.00000 (0/97640, ALFA)
T=0.00000 (0/97640, ALFA)
A=0.00001 (1/78700, PAGE_STUDY)
A=0.0002 (1/6404, 1000G_30x)
A=0.0002 (1/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LBR : 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 97640 G=1.00000 A=0.00000, T=0.00000
European Sub 86688 G=1.00000 A=0.00000, T=0.00000
African Sub 4188 G=1.0000 A=0.0000, T=0.0000
African Others Sub 168 G=1.000 A=0.000, T=0.000
African American Sub 4020 G=1.0000 A=0.0000, T=0.0000
Asian Sub 3308 G=1.0000 A=0.0000, T=0.0000
East Asian Sub 2682 G=1.0000 A=0.0000, T=0.0000
Other Asian Sub 626 G=1.000 A=0.000, T=0.000
Latin American 1 Sub 436 G=1.000 A=0.000, T=0.000
Latin American 2 Sub 928 G=1.000 A=0.000, T=0.000
South Asian Sub 280 G=1.000 A=0.000, T=0.000
Other Sub 1812 G=1.0000 A=0.0000, T=0.0000


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
gnomAD - Exomes Global Study-wide 247992 G=0.999964 A=0.000036
gnomAD - Exomes European Sub 134406 G=1.000000 A=0.000000
gnomAD - Exomes Asian Sub 47696 G=0.99983 A=0.00017
gnomAD - Exomes American Sub 33862 G=0.99997 A=0.00003
gnomAD - Exomes African Sub 16098 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 9912 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 6018 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140148 G=0.999993 T=0.000007
gnomAD - Genomes European Sub 75900 G=0.99999 T=0.00001
gnomAD - Genomes African Sub 42002 G=1.00000 T=0.00000
gnomAD - Genomes American Sub 13644 G=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2148 G=1.0000 T=0.0000
ExAC Global Study-wide 120576 G=0.999950 A=0.000050
ExAC Europe Sub 73004 G=1.00000 A=0.00000
ExAC Asian Sub 25072 G=0.99980 A=0.00020
ExAC American Sub 11576 G=0.99991 A=0.00009
ExAC African Sub 10016 G=1.00000 A=0.00000
ExAC Other Sub 908 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 97640 G=1.00000 A=0.00000, T=0.00000
Allele Frequency Aggregator European Sub 86688 G=1.00000 A=0.00000, T=0.00000
Allele Frequency Aggregator African Sub 4188 G=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator Asian Sub 3308 G=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator Other Sub 1812 G=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 928 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 436 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 280 G=1.000 A=0.000, T=0.000
The PAGE Study Global Study-wide 78700 G=0.99999 A=0.00001
The PAGE Study AfricanAmerican Sub 32514 G=1.00000 A=0.00000
The PAGE Study Mexican Sub 10810 G=1.00000 A=0.00000
The PAGE Study Asian Sub 8318 G=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7918 G=1.0000 A=0.0000
The PAGE Study NativeHawaiian Sub 4534 G=0.9998 A=0.0002
The PAGE Study Cuban Sub 4230 G=1.0000 A=0.0000
The PAGE Study Dominican Sub 3828 G=1.0000 A=0.0000
The PAGE Study CentralAmerican Sub 2450 G=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 G=1.0000 A=0.0000
The PAGE Study NativeAmerican Sub 1260 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
1000Genomes_30x Global Study-wide 6404 G=0.9998 A=0.0002
1000Genomes_30x African Sub 1786 G=1.0000 A=0.0000
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=0.9991 A=0.0009
1000Genomes_30x American Sub 980 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.9998 A=0.0002
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=0.9990 A=0.0010
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=1.000 A=0.000
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 1 NC_000001.11:g.225406664G>A
GRCh38.p14 chr 1 NC_000001.11:g.225406664G>T
GRCh37.p13 chr 1 NC_000001.10:g.225594366G>A
GRCh37.p13 chr 1 NC_000001.10:g.225594366G>T
LBR RefSeqGene NG_008099.1:g.27154C>T
LBR RefSeqGene NG_008099.1:g.27154C>A
Gene: LBR, lamin B receptor (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LBR transcript variant 1 NM_002296.4:c.1483C>T L [CTT] > F [TTT] Coding Sequence Variant
delta(14)-sterol reductase LBR NP_002287.2:p.Leu495Phe L (Leu) > F (Phe) Missense Variant
LBR transcript variant 1 NM_002296.4:c.1483C>A L [CTT] > I [ATT] Coding Sequence Variant
delta(14)-sterol reductase LBR NP_002287.2:p.Leu495Ile L (Leu) > I (Ile) Missense Variant
LBR transcript variant 2 NM_194442.3:c.1483C>T L [CTT] > F [TTT] Coding Sequence Variant
delta(14)-sterol reductase LBR NP_919424.1:p.Leu495Phe L (Leu) > F (Phe) Missense Variant
LBR transcript variant 2 NM_194442.3:c.1483C>A L [CTT] > I [ATT] Coding Sequence Variant
delta(14)-sterol reductase LBR NP_919424.1:p.Leu495Ile L (Leu) > I (Ile) Missense Variant
LBR transcript variant X5 XM_047420386.1:c. N/A Genic Downstream Transcript Variant
LBR transcript variant X1 XM_011544185.4:c.1483C>T L [CTT] > F [TTT] Coding Sequence Variant
delta(14)-sterol reductase LBR isoform X1 XP_011542487.1:p.Leu495Phe L (Leu) > F (Phe) Missense Variant
LBR transcript variant X1 XM_011544185.4:c.1483C>A L [CTT] > I [ATT] Coding Sequence Variant
delta(14)-sterol reductase LBR isoform X1 XP_011542487.1:p.Leu495Ile L (Leu) > I (Ile) Missense Variant
LBR transcript variant X2 XM_005273125.4:c.1357C>T L [CTT] > F [TTT] Coding Sequence Variant
delta(14)-sterol reductase LBR isoform X2 XP_005273182.1:p.Leu453Phe L (Leu) > F (Phe) Missense Variant
LBR transcript variant X2 XM_005273125.4:c.1357C>A L [CTT] > I [ATT] Coding Sequence Variant
delta(14)-sterol reductase LBR isoform X2 XP_005273182.1:p.Leu453Ile L (Leu) > I (Ile) Missense Variant
LBR transcript variant X3 XM_047420376.1:c.1357C>T L [CTT] > F [TTT] Coding Sequence Variant
delta(14)-sterol reductase LBR isoform X2 XP_047276332.1:p.Leu453Phe L (Leu) > F (Phe) Missense Variant
LBR transcript variant X3 XM_047420376.1:c.1357C>A L [CTT] > I [ATT] Coding Sequence Variant
delta(14)-sterol reductase LBR isoform X2 XP_047276332.1:p.Leu453Ile L (Leu) > I (Ile) Missense Variant
LBR transcript variant X4 XM_047420377.1:c.1357C>T L [CTT] > F [TTT] Coding Sequence Variant
delta(14)-sterol reductase LBR isoform X2 XP_047276333.1:p.Leu453Phe L (Leu) > F (Phe) Missense Variant
LBR transcript variant X4 XM_047420377.1:c.1357C>A L [CTT] > I [ATT] Coding Sequence Variant
delta(14)-sterol reductase LBR isoform X2 XP_047276333.1:p.Leu453Ile L (Leu) > I (Ile) 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.

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= A T
GRCh38.p14 chr 1 NC_000001.11:g.225406664= NC_000001.11:g.225406664G>A NC_000001.11:g.225406664G>T
GRCh37.p13 chr 1 NC_000001.10:g.225594366= NC_000001.10:g.225594366G>A NC_000001.10:g.225594366G>T
LBR RefSeqGene NG_008099.1:g.27154= NG_008099.1:g.27154C>T NG_008099.1:g.27154C>A
LBR transcript variant 1 NM_002296.4:c.1483= NM_002296.4:c.1483C>T NM_002296.4:c.1483C>A
LBR transcript variant 1 NM_002296.3:c.1483= NM_002296.3:c.1483C>T NM_002296.3:c.1483C>A
LBR transcript variant 2 NM_194442.3:c.1483= NM_194442.3:c.1483C>T NM_194442.3:c.1483C>A
LBR transcript variant 2 NM_194442.2:c.1483= NM_194442.2:c.1483C>T NM_194442.2:c.1483C>A
LBR transcript variant X1 XM_011544185.4:c.1483= XM_011544185.4:c.1483C>T XM_011544185.4:c.1483C>A
LBR transcript variant X1 XM_011544185.3:c.1483= XM_011544185.3:c.1483C>T XM_011544185.3:c.1483C>A
LBR transcript variant X1 XM_011544185.2:c.1483= XM_011544185.2:c.1483C>T XM_011544185.2:c.1483C>A
LBR transcript variant X1 XM_011544185.1:c.1483= XM_011544185.1:c.1483C>T XM_011544185.1:c.1483C>A
LBR transcript variant X2 XM_005273125.4:c.1357= XM_005273125.4:c.1357C>T XM_005273125.4:c.1357C>A
LBR transcript variant X2 XM_005273125.3:c.1357= XM_005273125.3:c.1357C>T XM_005273125.3:c.1357C>A
LBR transcript variant X2 XM_005273125.2:c.1357= XM_005273125.2:c.1357C>T XM_005273125.2:c.1357C>A
LBR transcript variant X1 XM_005273125.1:c.1357= XM_005273125.1:c.1357C>T XM_005273125.1:c.1357C>A
LBR transcript variant X4 XM_047420377.1:c.1357= XM_047420377.1:c.1357C>T XM_047420377.1:c.1357C>A
LBR transcript variant X3 XM_047420376.1:c.1357= XM_047420376.1:c.1357C>T XM_047420376.1:c.1357C>A
delta(14)-sterol reductase LBR NP_002287.2:p.Leu495= NP_002287.2:p.Leu495Phe NP_002287.2:p.Leu495Ile
delta(14)-sterol reductase LBR NP_919424.1:p.Leu495= NP_919424.1:p.Leu495Phe NP_919424.1:p.Leu495Ile
delta(14)-sterol reductase LBR isoform X1 XP_011542487.1:p.Leu495= XP_011542487.1:p.Leu495Phe XP_011542487.1:p.Leu495Ile
delta(14)-sterol reductase LBR isoform X2 XP_005273182.1:p.Leu453= XP_005273182.1:p.Leu453Phe XP_005273182.1:p.Leu453Ile
delta(14)-sterol reductase LBR isoform X2 XP_047276333.1:p.Leu453= XP_047276333.1:p.Leu453Phe XP_047276333.1:p.Leu453Ile
delta(14)-sterol reductase LBR isoform X2 XP_047276332.1:p.Leu453= XP_047276332.1:p.Leu453Phe XP_047276332.1:p.Leu453Ile
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#.

22 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1294886012 Aug 21, 2014 (142)
2 EVA_EXAC ss1686076995 Apr 01, 2015 (144)
3 ILLUMINA ss1946024956 Feb 12, 2016 (147)
4 ILLUMINA ss1958362124 Feb 12, 2016 (147)
5 HUMAN_LONGEVITY ss2170572713 Dec 20, 2016 (150)
6 GNOMAD ss2732310770 Nov 08, 2017 (151)
7 ILLUMINA ss3021185836 Nov 08, 2017 (151)
8 ILLUMINA ss3625564936 Oct 11, 2018 (152)
9 ILLUMINA ss3644520955 Oct 11, 2018 (152)
10 ILLUMINA ss3651531309 Oct 11, 2018 (152)
11 ILLUMINA ss3725110817 Jul 12, 2019 (153)
12 ILLUMINA ss3744061614 Jul 12, 2019 (153)
13 PAGE_CC ss3770875947 Jul 12, 2019 (153)
14 KHV_HUMAN_GENOMES ss3800412637 Jul 12, 2019 (153)
15 GNOMAD ss4012321590 Apr 27, 2021 (155)
16 TOPMED ss4485655441 Apr 27, 2021 (155)
17 TOPMED ss4485655442 Apr 27, 2021 (155)
18 EVA ss5325166905 Oct 17, 2022 (156)
19 1000G_HIGH_COVERAGE ss5520204871 Oct 17, 2022 (156)
20 EVA ss5847576171 Oct 17, 2022 (156)
21 EVA ss5912209931 Oct 17, 2022 (156)
22 EVA ss5939408368 Oct 17, 2022 (156)
23 1000Genomes NC_000001.10 - 225594366 Oct 11, 2018 (152)
24 1000Genomes_30x NC_000001.11 - 225406664 Oct 17, 2022 (156)
25 ExAC NC_000001.10 - 225594366 Oct 11, 2018 (152)
26 gnomAD - Genomes NC_000001.11 - 225406664 Apr 27, 2021 (155)
27 gnomAD - Exomes NC_000001.10 - 225594366 Jul 12, 2019 (153)
28 The PAGE Study NC_000001.11 - 225406664 Jul 12, 2019 (153)
29 TopMed

Submission ignored due to conflicting rows:
Row 49261776 (NC_000001.11:225406663:G:A 1/264690)
Row 49261777 (NC_000001.11:225406663:G:T 1/264690)

- Apr 27, 2021 (155)
30 TopMed

Submission ignored due to conflicting rows:
Row 49261776 (NC_000001.11:225406663:G:A 1/264690)
Row 49261777 (NC_000001.11:225406663:G:T 1/264690)

- Apr 27, 2021 (155)
31 ALFA NC_000001.11 - 225406664 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
5749006, 5315239, 1347446, ss1294886012, ss1686076995, ss1946024956, ss1958362124, ss2732310770, ss3021185836, ss3625564936, ss3644520955, ss3651531309, ss3744061614, ss5325166905, ss5847576171, ss5939408368 NC_000001.10:225594365:G:A NC_000001.11:225406663:G:A (self)
7730806, 97416, 1898247413, ss2170572713, ss3725110817, ss3770875947, ss3800412637, ss4485655441, ss5520204871, ss5912209931 NC_000001.11:225406663:G:A NC_000001.11:225406663:G:A (self)
41283012, 1898247413, ss4012321590, ss4485655442 NC_000001.11:225406663:G:T NC_000001.11:225406663: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 rs541202772

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