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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.

rs774903143

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:186209099-186209101 (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
delCA
Variation Type
Indel Insertion and Deletion
Frequency
delCA=0.000004 (1/251480, GnomAD_exome)
delCA=0.000008 (1/121410, ExAC)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CYP4V2 : Stop Gained
KLKB1 : 2KB Upstream Variant
Publications
0 citations
Genomic View
See rs on genome
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 251480 ACA=0.999996 delCA=0.000004
gnomAD - Exomes European Sub 135404 ACA=0.999993 delCA=0.000007
gnomAD - Exomes Asian Sub 49010 ACA=1.00000 delCA=0.00000
gnomAD - Exomes American Sub 34590 ACA=1.00000 delCA=0.00000
gnomAD - Exomes African Sub 16256 ACA=1.00000 delCA=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10080 ACA=1.00000 delCA=0.00000
gnomAD - Exomes Other Sub 6140 ACA=1.0000 delCA=0.0000
ExAC Global Study-wide 121410 ACA=0.999992 delCA=0.000008
ExAC Europe Sub 73354 ACA=0.99999 delCA=0.00001
ExAC Asian Sub 25166 ACA=1.00000 delCA=0.00000
ExAC American Sub 11578 ACA=1.00000 delCA=0.00000
ExAC African Sub 10406 ACA=1.00000 delCA=0.00000
ExAC Other Sub 906 ACA=1.000 delCA=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.186209100_186209101del
GRCh37.p13 chr 4 NC_000004.11:g.187130254_187130255del
KLKB1 RefSeqGene (LRG_565) NG_012095.2:g.5122_5123del
CYP4V2 RefSeqGene NG_007965.1:g.22581_22582del
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.1233_1234del YR [TACAG] > * [TAGA] Coding Sequence Variant
cytochrome P450 4V2 NP_997235.3:p.Tyr411_Arg4…

NP_997235.3:p.Tyr411_Arg412delinsTer

YR (TyrArg) > * (Ter) Stop Gained
CYP4V2 transcript variant X1 XM_005262935.5:c.1230_123…

XM_005262935.5:c.1230_1231del

YR [TACAG] > * [TAGA] Coding Sequence Variant
cytochrome P450 4V2 isoform X1 XP_005262992.1:p.Tyr410_A…

XP_005262992.1:p.Tyr410_Arg411delinsTer

YR (TyrArg) > * (Ter) Stop Gained
CYP4V2 transcript variant X2 XM_047450077.1:c.837_838d…

XM_047450077.1:c.837_838del

YR [TACAG] > * [TAGA] Coding Sequence Variant
cytochrome P450 4V2 isoform X2 XP_047306033.1:p.Tyr279_A…

XP_047306033.1:p.Tyr279_Arg280delinsTer

YR (TyrArg) > * (Ter) Stop Gained
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 ACA= delCA
GRCh38.p14 chr 4 NC_000004.12:g.186209099_186209101= NC_000004.12:g.186209100_186209101del
GRCh37.p13 chr 4 NC_000004.11:g.187130253_187130255= NC_000004.11:g.187130254_187130255del
KLKB1 RefSeqGene (LRG_565) NG_012095.2:g.5121_5123= NG_012095.2:g.5122_5123del
CYP4V2 RefSeqGene NG_007965.1:g.22580_22582= NG_007965.1:g.22581_22582del
CYP4V2 transcript NM_207352.4:c.1232_1234= NM_207352.4:c.1233_1234del
CYP4V2 transcript NM_207352.3:c.1232_1234= NM_207352.3:c.1233_1234del
CYP4V2 transcript variant X1 XM_005262935.5:c.1229_1231= XM_005262935.5:c.1230_1231del
CYP4V2 transcript variant X1 XM_005262935.4:c.1229_1231= XM_005262935.4:c.1230_1231del
CYP4V2 transcript variant X1 XM_005262935.3:c.1229_1231= XM_005262935.3:c.1230_1231del
CYP4V2 transcript variant X1 XM_005262935.2:c.1229_1231= XM_005262935.2:c.1230_1231del
CYP4V2 transcript variant X1 XM_005262935.1:c.1229_1231= XM_005262935.1:c.1230_1231del
CYP4V2 transcript variant X2 XM_047450077.1:c.836_838= XM_047450077.1:c.837_838del
cytochrome P450 4V2 NP_997235.3:p.Tyr411_Arg412= NP_997235.3:p.Tyr411_Arg412delinsTer
cytochrome P450 4V2 isoform X1 XP_005262992.1:p.Tyr410_Arg411= XP_005262992.1:p.Tyr410_Arg411delinsTer
cytochrome P450 4V2 isoform X2 XP_047306033.1:p.Tyr279_Arg280= XP_047306033.1:p.Tyr279_Arg280delinsTer
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, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1711778839 Apr 01, 2015 (144)
2 GNOMAD ss2734857559 Nov 08, 2017 (151)
3 ExAC NC_000004.11 - 187130253 Oct 12, 2018 (152)
4 gnomAD - Exomes NC_000004.11 - 187130253 Jul 13, 2019 (153)
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
7699404, 3971500, ss1711778839, ss2734857559 NC_000004.11:187130252:AC: NC_000004.12:186209098:ACA: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 rs774903143

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