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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.

rs1467173859

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:54664222 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000011 (3/264690, TOPMED)
A=0.000007 (1/140230, GnomAD)
A=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LILRB4 : 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 14050 G=1.00000 A=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 G=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 G=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 G=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 496 G=1.000 A=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 A=0.000011
gnomAD - Genomes Global Study-wide 140230 G=0.999993 A=0.000007
gnomAD - Genomes European Sub 75924 G=0.99999 A=0.00001
gnomAD - Genomes African Sub 42028 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 13666 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 14050 G=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 9690 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2898 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Other Sub 496 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=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 19 NC_000019.10:g.54664222G>A
GRCh37.p13 chr 19 fix patch HG1079_PATCH NW_004166865.1:g.638589G>A
GRCh38.p14 chr 19 alt locus HSCHR19LRC_PGF2_CTG3_1 NW_003571061.2:g.390726G>A
GRCh37.p13 chr 19 novel patch HSCHR19LRC_PGF2_CTG1 NW_003571061.1:g.390725G>A
GRCh38.p14 chr 19 alt locus HSCHR19_4_CTG3_1 NT_187693.1:g.646787G>A
GRCh37.p13 chr 19 NC_000019.9:g.55175673G>A
GRCh38.p14 chr 19 alt locus HSCHR19LRC_PGF1_CTG3_1 NW_003571060.1:g.569104G>A
GRCh38.p14 chr 19 alt locus HSCHR19LRC_COX1_CTG3_1 NW_003571054.1:g.570625G>A
Gene: LILRB4, leukocyte immunoglobulin like receptor B4 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LILRB4 transcript variant 10 NM_001394937.1:c.356G>A S [AGT] > N [AAT] Coding Sequence Variant
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 10 precursor NP_001381866.1:p.Ser119Asn S (Ser) > N (Asn) Missense Variant
LILRB4 transcript variant 12 NM_001394939.1:c.392G>A S [AGT] > N [AAT] Coding Sequence Variant
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 12 precursor NP_001381868.1:p.Ser131Asn S (Ser) > N (Asn) Missense Variant
LILRB4 transcript variant 11 NM_001394938.1:c.356G>A S [AGT] > N [AAT] Coding Sequence Variant
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 11 precursor NP_001381867.1:p.Ser119Asn S (Ser) > N (Asn) Missense Variant
LILRB4 transcript variant 4 NM_001278429.4:c.356G>A S [AGT] > N [AAT] Coding Sequence Variant
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 4 precursor NP_001265358.3:p.Ser119Asn S (Ser) > N (Asn) Missense Variant
LILRB4 transcript variant 9 NM_001394936.1:c.356G>A S [AGT] > N [AAT] Coding Sequence Variant
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 9 precursor NP_001381865.1:p.Ser119Asn S (Ser) > N (Asn) Missense Variant
LILRB4 transcript variant 6 NM_001394933.1:c.392G>A S [AGT] > N [AAT] Coding Sequence Variant
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 6 precursor NP_001381862.1:p.Ser131Asn S (Ser) > N (Asn) Missense Variant
LILRB4 transcript variant 7 NM_001394934.1:c.392G>A S [AGT] > N [AAT] Coding Sequence Variant
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 7 precursor NP_001381863.1:p.Ser131Asn S (Ser) > N (Asn) Missense Variant
LILRB4 transcript variant 8 NM_001394935.1:c.392G>A S [AGT] > N [AAT] Coding Sequence Variant
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 8 precursor NP_001381864.1:p.Ser131Asn S (Ser) > N (Asn) Missense Variant
LILRB4 transcript variant 5 NM_001278430.4:c.392G>A S [AGT] > N [AAT] Coding Sequence Variant
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 5 precursor NP_001265359.2:p.Ser131Asn S (Ser) > N (Asn) Missense Variant
LILRB4 transcript variant 3 NM_001278428.4:c.392G>A S [AGT] > N [AAT] Coding Sequence Variant
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 3 precursor NP_001265357.2:p.Ser131Asn S (Ser) > N (Asn) Missense Variant
LILRB4 transcript variant 2 NM_001278427.4:c.392G>A S [AGT] > N [AAT] Coding Sequence Variant
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor NP_001265356.2:p.Ser131Asn S (Ser) > N (Asn) Missense Variant
LILRB4 transcript variant 1 NM_001278426.4:c.392G>A S [AGT] > N [AAT] Coding Sequence Variant
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 1 precursor NP_001265355.2:p.Ser131Asn S (Ser) > N (Asn) Missense Variant
LILRB4 transcript variant X1 XM_017026216.2:c.392G>A S [AGT] > N [AAT] Coding Sequence Variant
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform X1 XP_016881705.2:p.Ser131Asn S (Ser) > N (Asn) Missense Variant
LILRB4 transcript variant X2 XM_047438100.1:c.356G>A S [AGT] > N [AAT] Coding Sequence Variant
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform X2 XP_047294056.1:p.Ser119Asn S (Ser) > N (Asn) Missense Variant
LILRB4 transcript variant X3 XM_047438101.1:c.356G>A S [AGT] > N [AAT] Coding Sequence Variant
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform X3 XP_047294057.1:p.Ser119Asn S (Ser) > N (Asn) Missense Variant
LILRB4 transcript variant X4 XM_047438102.1:c.392G>A S [AGT] > N [AAT] Coding Sequence Variant
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform X4 XP_047294058.1:p.Ser131Asn S (Ser) > N (Asn) Missense Variant
LILRB4 transcript variant X5 XM_047438103.1:c.131G>A S [AGT] > N [AAT] Coding Sequence Variant
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform X5 XP_047294059.1:p.Ser44Asn S (Ser) > N (Asn) 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
GRCh38.p14 chr 19 NC_000019.10:g.54664222= NC_000019.10:g.54664222G>A
GRCh37.p13 chr 19 fix patch HG1079_PATCH NW_004166865.1:g.638589= NW_004166865.1:g.638589G>A
GRCh38.p14 chr 19 alt locus HSCHR19LRC_PGF2_CTG3_1 NW_003571061.2:g.390726= NW_003571061.2:g.390726G>A
GRCh37.p13 chr 19 novel patch HSCHR19LRC_PGF2_CTG1 NW_003571061.1:g.390725= NW_003571061.1:g.390725G>A
GRCh38.p14 chr 19 alt locus HSCHR19_4_CTG3_1 NT_187693.1:g.646787= NT_187693.1:g.646787G>A
GRCh37.p13 chr 19 NC_000019.9:g.55175673= NC_000019.9:g.55175673G>A
GRCh38.p14 chr 19 alt locus HSCHR19LRC_PGF1_CTG3_1 NW_003571060.1:g.569104= NW_003571060.1:g.569104G>A
GRCh38.p14 chr 19 alt locus HSCHR19LRC_COX1_CTG3_1 NW_003571054.1:g.570625= NW_003571054.1:g.570625G>A
LILRB4 transcript variant 3 NM_001278428.4:c.392= NM_001278428.4:c.392G>A
LILRB4 transcript variant 3 NM_001278428.3:c.392= NM_001278428.3:c.392G>A
LILRB4 transcript variant 3 NM_001278428.2:c.392= NM_001278428.2:c.392G>A
LILRB4 transcript variant 1 NM_001278426.4:c.392= NM_001278426.4:c.392G>A
LILRB4 transcript variant 1 NM_001278426.3:c.392= NM_001278426.3:c.392G>A
LILRB4 transcript variant 1 NM_001278426.2:c.392= NM_001278426.2:c.392G>A
LILRB4 transcript variant 2 NM_001278427.4:c.392= NM_001278427.4:c.392G>A
LILRB4 transcript variant 2 NM_001278427.3:c.392= NM_001278427.3:c.392G>A
LILRB4 transcript variant 2 NM_001278427.2:c.392= NM_001278427.2:c.392G>A
LILRB4 transcript variant 4 NM_001278429.4:c.356= NM_001278429.4:c.356G>A
LILRB4 transcript variant 4 NM_001278429.3:c.479= NM_001278429.3:c.479G>A
LILRB4 transcript variant 4 NM_001278429.2:c.479= NM_001278429.2:c.479G>A
LILRB4 transcript variant 5 NM_001278430.4:c.392= NM_001278430.4:c.392G>A
LILRB4 transcript variant 5 NM_001278430.3:c.392= NM_001278430.3:c.392G>A
LILRB4 transcript variant 5 NM_001278430.2:c.392= NM_001278430.2:c.392G>A
LILRB4 transcript variant 1 NM_006847.3:c.392= NM_006847.3:c.392G>A
LILRB4 transcript variant X1 XM_017026216.2:c.392= XM_017026216.2:c.392G>A
LILRB4 transcript variant X2 XM_017026216.1:c.515= XM_017026216.1:c.515G>A
LILRB4 transcript variant 7 NM_001394934.1:c.392= NM_001394934.1:c.392G>A
LILRB4 transcript NM_006847.2:c.392= NM_006847.2:c.392G>A
LILRB4 transcript variant 6 NM_001394933.1:c.392= NM_001394933.1:c.392G>A
LILRB4 transcript variant X2 XM_047438100.1:c.356= XM_047438100.1:c.356G>A
LILRB4 transcript variant X3 XM_047438101.1:c.356= XM_047438101.1:c.356G>A
LILRB4 transcript variant X5 XM_047438103.1:c.131= XM_047438103.1:c.131G>A
LILRB4 transcript variant 11 NM_001394938.1:c.356= NM_001394938.1:c.356G>A
LILRB4 transcript NM_006847.1:c.392= NM_006847.1:c.392G>A
LILRB4 transcript variant 8 NM_001394935.1:c.392= NM_001394935.1:c.392G>A
LILRB4 transcript variant 9 NM_001394936.1:c.356= NM_001394936.1:c.356G>A
LILRB4 transcript variant 2 NM_001081438.1:c.392= NM_001081438.1:c.392G>A
LILRB4 transcript variant 10 NM_001394937.1:c.356= NM_001394937.1:c.356G>A
LILRB4 transcript variant 12 NM_001394939.1:c.392= NM_001394939.1:c.392G>A
LILRB4 transcript variant X4 XM_047438102.1:c.392= XM_047438102.1:c.392G>A
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 3 precursor NP_001265357.2:p.Ser131= NP_001265357.2:p.Ser131Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 1 precursor NP_001265355.2:p.Ser131= NP_001265355.2:p.Ser131Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor NP_001265356.2:p.Ser131= NP_001265356.2:p.Ser131Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 4 precursor NP_001265358.3:p.Ser119= NP_001265358.3:p.Ser119Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 5 precursor NP_001265359.2:p.Ser131= NP_001265359.2:p.Ser131Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform X1 XP_016881705.2:p.Ser131= XP_016881705.2:p.Ser131Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 7 precursor NP_001381863.1:p.Ser131= NP_001381863.1:p.Ser131Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 6 precursor NP_001381862.1:p.Ser131= NP_001381862.1:p.Ser131Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform X2 XP_047294056.1:p.Ser119= XP_047294056.1:p.Ser119Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform X3 XP_047294057.1:p.Ser119= XP_047294057.1:p.Ser119Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform X5 XP_047294059.1:p.Ser44= XP_047294059.1:p.Ser44Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 11 precursor NP_001381867.1:p.Ser119= NP_001381867.1:p.Ser119Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 8 precursor NP_001381864.1:p.Ser131= NP_001381864.1:p.Ser131Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 9 precursor NP_001381865.1:p.Ser119= NP_001381865.1:p.Ser119Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 10 precursor NP_001381866.1:p.Ser119= NP_001381866.1:p.Ser119Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 12 precursor NP_001381868.1:p.Ser131= NP_001381868.1:p.Ser131Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform X4 XP_047294058.1:p.Ser131= XP_047294058.1:p.Ser131Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 1 precursor NP_001265355.1:p.Ser131= NP_001265355.1:p.Ser131Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 2 precursor NP_001265356.1:p.Ser131= NP_001265356.1:p.Ser131Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 3 precursor NP_001265357.1:p.Ser131= NP_001265357.1:p.Ser131Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 4 NP_001265358.1:p.Ser160= NP_001265358.1:p.Ser160Asn
leukocyte immunoglobulin-like receptor subfamily B member 4 isoform 5 precursor NP_001265359.1:p.Ser131= NP_001265359.1:p.Ser131Asn
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#.

2 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss4333252524 Apr 27, 2021 (155)
2 TOPMED ss5078673132 Apr 27, 2021 (155)
3 gnomAD - Genomes NC_000019.10 - 54664222 Apr 27, 2021 (155)
4 TopMed NC_000019.10 - 54664222 Apr 27, 2021 (155)
5 ALFA NC_000019.10 - 54664222 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
543425745, 294218796, 6648126889, ss4333252524, ss5078673132 NC_000019.10:54664221:G:A NC_000019.10:54664221: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.

No publications for rs1467173859

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