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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.


Current Build 155

Released April 9, 2021

Homo sapiens
chr4:186199040-186199041 (GRCh38.p13) 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.

delA / dupA
Variation Type
Indel Insertion and Deletion
delA=0.000004 (1/251416, GnomAD_exome)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CYP4V2 : Frameshift Variant
1 citation
Genomic View
See rs on genome

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.p13 chr 4 NC_000004.12:g.186199041del
GRCh38.p13 chr 4 NC_000004.12:g.186199041dup
GRCh37.p13 chr 4 NC_000004.11:g.187120195del
GRCh37.p13 chr 4 NC_000004.11:g.187120195dup
CYP4V2 RefSeqGene NG_007965.1:g.12522del
CYP4V2 RefSeqGene NG_007965.1:g.12522dup
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.759del E [GAA] > D [GA] Coding Sequence Variant
cytochrome P450 4V2 NP_997235.3:p.Glu253fs E (Glu) > D (Asp) Frameshift Variant
CYP4V2 transcript NM_207352.4:c.759dup H [CAC] > T [ACAC] Coding Sequence Variant
cytochrome P450 4V2 NP_997235.3:p.His254fs H (His) > T (Thr) Frameshift Variant
CYP4V2 transcript variant X2 XM_017008037.1:c.363del E [GAA] > D [GA] Coding Sequence Variant
cytochrome P450 4V2 isoform X2 XP_016863526.1:p.Glu121fs E (Glu) > D (Asp) Frameshift Variant
CYP4V2 transcript variant X2 XM_017008037.1:c.363dup H [CAC] > T [ACAC] Coding Sequence Variant
cytochrome P450 4V2 isoform X2 XP_016863526.1:p.His122fs H (His) > T (Thr) Frameshift Variant
CYP4V2 transcript variant X1 XM_005262935.4:c.759del E [GAA] > D [GA] Coding Sequence Variant
cytochrome P450 4V2 isoform X1 XP_005262992.1:p.Glu253fs E (Glu) > D (Asp) Frameshift Variant
CYP4V2 transcript variant X1 XM_005262935.4:c.759dup H [CAC] > T [ACAC] Coding Sequence Variant
cytochrome P450 4V2 isoform X1 XP_005262992.1:p.His254fs H (His) > T (Thr) Frameshift Variant

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: dupA (allele ID: 47875 )
ClinVar Accession Disease Names Clinical Significance
RCV000032546.2 Bietti crystalline corneoretinal dystrophy Pathogenic

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").

Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 251416 AA=0.999996 delA=0.000004
gnomAD - Exomes European Sub 135350 AA=1.000000 delA=0.000000
gnomAD - Exomes Asian Sub 49006 AA=0.99998 delA=0.00002
gnomAD - Exomes American Sub 34590 AA=1.00000 delA=0.00000
gnomAD - Exomes African Sub 16256 AA=1.00000 delA=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10078 AA=1.00000 delA=0.00000
gnomAD - Exomes Other Sub 6136 AA=1.0000 delA=0.0000

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 AA= delA dupA
GRCh38.p13 chr 4 NC_000004.12:g.186199040_186199041= NC_000004.12:g.186199041del NC_000004.12:g.186199041dup
GRCh37.p13 chr 4 NC_000004.11:g.187120194_187120195= NC_000004.11:g.187120195del NC_000004.11:g.187120195dup
CYP4V2 RefSeqGene NG_007965.1:g.12521_12522= NG_007965.1:g.12522del NG_007965.1:g.12522dup
CYP4V2 transcript NM_207352.4:c.758_759= NM_207352.4:c.759del NM_207352.4:c.759dup
CYP4V2 transcript NM_207352.3:c.758_759= NM_207352.3:c.759del NM_207352.3:c.759dup
CYP4V2 transcript variant X1 XM_005262935.4:c.758_759= XM_005262935.4:c.759del XM_005262935.4:c.759dup
CYP4V2 transcript variant X1 XM_005262935.1:c.758_759= XM_005262935.1:c.759del XM_005262935.1:c.759dup
CYP4V2 transcript variant X2 XM_017008037.1:c.362_363= XM_017008037.1:c.363del XM_017008037.1:c.363dup
cytochrome P450 4V2 NP_997235.3:p.Glu253= NP_997235.3:p.Glu253fs NP_997235.3:p.His254fs
cytochrome P450 4V2 isoform X1 XP_005262992.1:p.Glu253= XP_005262992.1:p.Glu253fs XP_005262992.1:p.His254fs
cytochrome P450 4V2 isoform X2 XP_016863526.1:p.Glu121= XP_016863526.1:p.Glu121fs XP_016863526.1:p.His122fs

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#.

1 SubSNP, 1 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 GENEREVIEWS ss511341851 Dec 19, 2013 (138)
2 gnomAD - Exomes NC_000004.11 - 187120194 Jul 13, 2019 (153)
3 ClinVar RCV000032546.2 Oct 12, 2018 (152)

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
3971236 NC_000004.11:187120193:A: NC_000004.12:186199039:AA:A (self)
RCV000032546.2 NC_000004.12:186199039:AA:AAA NC_000004.12:186199039:AA:AAA (self)
ss511341851 NC_000004.12:186199041::A NC_000004.12:186199039:AA:AAA (self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs199476192
PMID Title Author Year Journal
22497028 Bietti Crystalline Dystrophy Vargas M et al. 1993 GeneReviews®

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.post596+ae089ad