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dbSNP Short Genetic Variations

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.

rs558238506

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:186209179 (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=0.000091 (24/264690, TOPMED)
A=0.000040 (10/251480, GnomAD_exome)
A=0.000079 (11/140124, GnomAD) (+ 4 more)
A=0.000041 (5/121400, ExAC)
A=0.00000 (0/14050, ALFA)
A=0.0003 (2/6404, 1000G_30x)
A=0.0002 (1/5008, 1000G)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CYP4V2 : Missense Variant
KLKB1 : 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 30400 G=0.99993 A=0.00007
European Sub 19768 G=1.00000 A=0.00000
African Sub 7736 G=0.9997 A=0.0003
African Others Sub 298 G=1.000 A=0.000
African American Sub 7438 G=0.9997 A=0.0003
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 1930 G=1.0000 A=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
TopMed Global Study-wide 264690 G=0.999909 A=0.000091
gnomAD - Exomes Global Study-wide 251480 G=0.999960 A=0.000040
gnomAD - Exomes European Sub 135404 G=1.000000 A=0.000000
gnomAD - Exomes Asian Sub 49010 G=0.99996 A=0.00004
gnomAD - Exomes American Sub 34590 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16256 G=0.99951 A=0.00049
gnomAD - Exomes Ashkenazi Jewish Sub 10080 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6140 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140124 G=0.999921 A=0.000079
gnomAD - Genomes European Sub 75886 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 42000 G=0.99976 A=0.00024
gnomAD - Genomes American Sub 13648 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3314 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3128 G=0.9997 A=0.0003
gnomAD - Genomes Other Sub 2148 G=1.0000 A=0.0000
ExAC Global Study-wide 121400 G=0.999959 A=0.000041
ExAC Europe Sub 73346 G=1.00000 A=0.00000
ExAC Asian Sub 25166 G=0.99996 A=0.00004
ExAC American Sub 11578 G=1.00000 A=0.00000
ExAC African Sub 10404 G=0.99962 A=0.00038
ExAC Other Sub 906 G=1.000 A=0.000
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
1000Genomes_30x Global Study-wide 6404 G=0.9997 A=0.0003
1000Genomes_30x African Sub 1786 G=0.9989 A=0.0011
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=1.0000 A=0.0000
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=0.9992 A=0.0008
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
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 4 NC_000004.12:g.186209179G>A
GRCh37.p13 chr 4 NC_000004.11:g.187130333G>A
KLKB1 RefSeqGene (LRG_565) NG_012095.2:g.5201G>A
CYP4V2 RefSeqGene NG_007965.1:g.22660G>A
Gene: KLKB1, kallikrein B1 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
KLKB1 transcript variant 1 NM_000892.5:c. N/A N/A
KLKB1 transcript variant 2 NM_001318394.2:c. N/A N/A
KLKB1 transcript variant 3 NM_001318396.2:c. N/A N/A
KLKB1 transcript variant X3 XM_047415661.1:c. N/A Upstream Transcript Variant
KLKB1 transcript variant X1 XM_011531930.3:c. N/A N/A
KLKB1 transcript variant X2 XM_017008181.2:c. N/A N/A
KLKB1 transcript variant X4 XM_017008182.2:c. N/A N/A
KLKB1 transcript variant X5 XM_017008183.2:c. N/A N/A
KLKB1 transcript variant X6 XM_017008184.2:c. N/A N/A
Gene: CYP4V2, cytochrome P450 family 4 subfamily V member 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CYP4V2 transcript NM_207352.4:c.1312G>A E [GAG] > K [AAG] Coding Sequence Variant
cytochrome P450 4V2 NP_997235.3:p.Glu438Lys E (Glu) > K (Lys) Missense Variant
CYP4V2 transcript variant X1 XM_005262935.5:c.1309G>A E [GAG] > K [AAG] Coding Sequence Variant
cytochrome P450 4V2 isoform X1 XP_005262992.1:p.Glu437Lys E (Glu) > K (Lys) Missense Variant
CYP4V2 transcript variant X2 XM_047450077.1:c.916G>A E [GAG] > K [AAG] Coding Sequence Variant
cytochrome P450 4V2 isoform X2 XP_047306033.1:p.Glu306Lys E (Glu) > K (Lys) 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: A (allele ID: 829025 )
ClinVar Accession Disease Names Clinical Significance
RCV001058545.5 not provided Uncertain-Significance
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 4 NC_000004.12:g.186209179= NC_000004.12:g.186209179G>A
GRCh37.p13 chr 4 NC_000004.11:g.187130333= NC_000004.11:g.187130333G>A
KLKB1 RefSeqGene (LRG_565) NG_012095.2:g.5201= NG_012095.2:g.5201G>A
CYP4V2 RefSeqGene NG_007965.1:g.22660= NG_007965.1:g.22660G>A
CYP4V2 transcript NM_207352.4:c.1312= NM_207352.4:c.1312G>A
CYP4V2 transcript NM_207352.3:c.1312= NM_207352.3:c.1312G>A
CYP4V2 transcript variant X1 XM_005262935.5:c.1309= XM_005262935.5:c.1309G>A
CYP4V2 transcript variant X1 XM_005262935.4:c.1309= XM_005262935.4:c.1309G>A
CYP4V2 transcript variant X1 XM_005262935.3:c.1309= XM_005262935.3:c.1309G>A
CYP4V2 transcript variant X1 XM_005262935.2:c.1309= XM_005262935.2:c.1309G>A
CYP4V2 transcript variant X1 XM_005262935.1:c.1309= XM_005262935.1:c.1309G>A
CYP4V2 transcript variant X2 XM_047450077.1:c.916= XM_047450077.1:c.916G>A
cytochrome P450 4V2 NP_997235.3:p.Glu438= NP_997235.3:p.Glu438Lys
cytochrome P450 4V2 isoform X1 XP_005262992.1:p.Glu437= XP_005262992.1:p.Glu437Lys
cytochrome P450 4V2 isoform X2 XP_047306033.1:p.Glu306= XP_047306033.1:p.Glu306Lys
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#.

12 SubSNP, 7 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1313431675 Aug 21, 2014 (142)
2 EVA_EXAC ss1687715793 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2270466610 Dec 20, 2016 (150)
4 GNOMAD ss2734857581 Nov 08, 2017 (151)
5 GNOMAD ss2747339058 Nov 08, 2017 (151)
6 GNOMAD ss2819830513 Nov 08, 2017 (151)
7 TOPMED ss4645867453 Apr 26, 2021 (155)
8 1000G_HIGH_COVERAGE ss5262447327 Oct 13, 2022 (156)
9 EVA ss5354878605 Oct 13, 2022 (156)
10 1000G_HIGH_COVERAGE ss5545295924 Oct 13, 2022 (156)
11 SANFORD_IMAGENETICS ss5636929403 Oct 13, 2022 (156)
12 EVA ss5867121971 Oct 13, 2022 (156)
13 1000Genomes NC_000004.11 - 187130333 Oct 12, 2018 (152)
14 1000Genomes_30x NC_000004.12 - 186209179 Oct 13, 2022 (156)
15 ExAC NC_000004.11 - 187130333 Oct 12, 2018 (152)
16 gnomAD - Genomes NC_000004.12 - 186209179 Apr 26, 2021 (155)
17 gnomAD - Exomes NC_000004.11 - 187130333 Jul 13, 2019 (153)
18 TopMed NC_000004.12 - 186209179 Apr 26, 2021 (155)
19 ALFA NC_000004.12 - 186209179 Apr 26, 2021 (155)
20 ClinVar RCV001058545.5 Oct 13, 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
24969684, 7699423, 3971522, ss1313431675, ss1687715793, ss2734857581, ss2747339058, ss2819830513, ss5354878605, ss5636929403 NC_000004.11:187130332:G:A NC_000004.12:186209178:G:A (self)
RCV001058545.5, 32821859, 176638391, 483245009, 6789222036, ss2270466610, ss4645867453, ss5262447327, ss5545295924, ss5867121971 NC_000004.12:186209178:G:A NC_000004.12:186209178: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 rs558238506

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