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dbSNP Short Genetic Variations

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 153

Released July 9, 2019

Homo sapiens
chr19:15540506 (GRCh38.p12) 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.

G>A / G>T
Variation Type
SNV Single Nucleotide Variation
A=0.00002 (2/125568, TOPMED)
A=0.00004 (5/121162, ExAC)
A=0.0000 (2/78698, PAGE_STUDY) (+ 2 more)
A=0.0000 (1/31392, GnomAD)
A=0.000 (1/5008, 1000G)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CYP4F22 : Missense 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.p12 chr 19 NC_000019.10:g.15540506G>A
GRCh38.p12 chr 19 NC_000019.10:g.15540506G>T
GRCh37.p13 chr 19 NC_000019.9:g.15651317G>A
GRCh37.p13 chr 19 NC_000019.9:g.15651317G>T
CYP4F22 RefSeqGene NG_007987.1:g.36982G>A
CYP4F22 RefSeqGene NG_007987.1:g.36982G>T
Gene: CYP4F22, cytochrome P450 family 4 subfamily F member 22 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CYP4F22 transcript NM_173483.4:c.728G>A R [CGC] > H [CAC] Coding Sequence Variant
cytochrome P450 4F22 NP_775754.2:p.Arg243His R (Arg) > H (His) Missense Variant
CYP4F22 transcript NM_173483.4:c.728G>T R [CGC] > L [CTC] Coding Sequence Variant
cytochrome P450 4F22 NP_775754.2:p.Arg243Leu R (Arg) > L (Leu) Missense Variant
CYP4F22 transcript variant X1 XM_011527692.2:c.728G>A R [CGC] > H [CAC] Coding Sequence Variant
cytochrome P450 4F22 isoform X1 XP_011525994.1:p.Arg243His R (Arg) > H (His) Missense Variant
CYP4F22 transcript variant X1 XM_011527692.2:c.728G>T R [CGC] > L [CTC] Coding Sequence Variant
cytochrome P450 4F22 isoform X1 XP_011525994.1:p.Arg243Leu R (Arg) > L (Leu) Missense Variant
CYP4F22 transcript variant X2 XM_011527693.2:c.728G>A R [CGC] > H [CAC] Coding Sequence Variant
cytochrome P450 4F22 isoform X1 XP_011525995.1:p.Arg243His R (Arg) > H (His) Missense Variant
CYP4F22 transcript variant X2 XM_011527693.2:c.728G>T R [CGC] > L [CTC] Coding Sequence Variant
cytochrome P450 4F22 isoform X1 XP_011525995.1:p.Arg243Leu R (Arg) > L (Leu) Missense 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: A (allele ID: 15950 )
ClinVar Accession Disease Names Clinical Significance
RCV000000959.2 Autosomal recessive congenital ichthyosis 5 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
TopMed Global Study-wide 125568 G=0.99998 A=0.00002
ExAC Global Study-wide 121162 G=0.99996 A=0.00004
ExAC Europe Sub 73170 G=0.9999 A=0.0001
ExAC Asian Sub 25144 G=1.0000 A=0.0000
ExAC American Sub 11570 G=1.0000 A=0.0000
ExAC African Sub 10370 G=0.9999 A=0.0001
ExAC Other Sub 908 G=1.00 A=0.00
The PAGE Study Global Study-wide 78698 G=1.0000 A=0.0000
The PAGE Study AfricanAmerican Sub 32512 G=1.0000 A=0.0000
The PAGE Study Mexican Sub 10810 G=0.9999 A=0.0001
The PAGE Study Asian Sub 8318 G=1.000 A=0.000
The PAGE Study PuertoRican Sub 7918 G=1.000 A=0.000
The PAGE Study NativeHawaiian Sub 4534 G=1.000 A=0.000
The PAGE Study Cuban Sub 4230 G=1.000 A=0.000
The PAGE Study Dominican Sub 3828 G=1.000 A=0.000
The PAGE Study CentralAmerican Sub 2450 G=1.000 A=0.000
The PAGE Study SouthAmerican Sub 1982 G=1.000 A=0.000
The PAGE Study NativeAmerican Sub 1260 G=1.000 A=0.000
The PAGE Study SouthAsian Sub 856 G=1.00 A=0.00
gnomAD - Genomes Global Study-wide 31392 G=1.0000 A=0.0000
gnomAD - Genomes European Sub 18896 G=1.0000 A=0.0000
gnomAD - Genomes African Sub 8710 G=1.000 A=0.000
gnomAD - Genomes East Asian Sub 1560 G=1.000 A=0.000
gnomAD - Genomes Other Sub 1088 G=1.000 A=0.000
gnomAD - Genomes American Sub 848 G=1.00 A=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=1.00 A=0.00
1000Genomes Global Study-wide 5008 G=1.000 A=0.000
1000Genomes African Sub 1322 G=1.000 A=0.000
1000Genomes East Asian Sub 1008 G=1.000 A=0.000
1000Genomes Europe Sub 1006 G=0.999 A=0.001
1000Genomes South Asian Sub 978 G=1.00 A=0.00
1000Genomes American Sub 694 G=1.00 A=0.00

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 Note
GRCh38.p12 chr 19 NC_000019.10:g.15...






GRCh37.p13 chr 19 NC_000019.9:g.156...






CYP4F22 RefSeqGene NG_007987.1:g.36982= NG_007987.1:g.369...




CYP4F22 transcript NM_173483.3:c.728= NM_173483.3:c.728G>A NM_173483.3:c.728G>T
CYP4F22 transcript NM_173483.4:c.728= NM_173483.4:c.728G>A NM_173483.4:c.728G>T
CYP4F22 transcript variant X1 XM_011527692.2:c....






CYP4F22 transcript variant X2 XM_011527693.2:c....






cytochrome P450 4F22 NP_775754.2:p.Arg...






cytochrome P450 4F22 isoform X1 XP_011525994.1:p....






cytochrome P450 4F22 isoform X1 XP_011525995.1:p....







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#.

19 SubSNP, 7 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss252841400 Aug 10, 2010 (132)
2 1000GENOMES ss1362502731 Aug 21, 2014 (142)
3 EVA_EXAC ss1693439202 Apr 01, 2015 (144)
4 ILLUMINA ss1946529755 Feb 12, 2016 (147)
5 ILLUMINA ss1959846515 Feb 12, 2016 (147)
6 TOPMED ss2390070384 Dec 20, 2016 (150)
7 GNOMAD ss2743740333 Nov 08, 2017 (151)
8 GNOMAD ss2750105953 Nov 08, 2017 (151)
9 GNOMAD ss2960912777 Nov 08, 2017 (151)
10 AFFY ss2985134849 Nov 08, 2017 (151)
11 ILLUMINA ss3021887078 Nov 08, 2017 (151)
12 TOPMED ss3288912079 Nov 08, 2017 (151)
13 ILLUMINA ss3625738025 Oct 12, 2018 (152)
14 ILLUMINA ss3644718350 Oct 12, 2018 (152)
15 ILLUMINA ss3652311851 Oct 12, 2018 (152)
16 ILLUMINA ss3653906721 Oct 12, 2018 (152)
17 ILLUMINA ss3725713712 Jul 13, 2019 (153)
18 ILLUMINA ss3744164403 Jul 13, 2019 (153)
19 PAGE_CC ss3772001943 Jul 13, 2019 (153)
20 1000Genomes NC_000019.9 - 15651317 Oct 12, 2018 (152)
21 ExAC NC_000019.9 - 15651317 Oct 12, 2018 (152)
22 gnomAD - Genomes NC_000019.9 - 15651317 Jul 13, 2019 (153)
23 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 13054573 (NC_000019.9:15651316:G:G 251397/251406, NC_000019.9:15651316:G:A 9/251406)
Row 13054574 (NC_000019.9:15651316:G:G 251405/251406, NC_000019.9:15651316:G:T 1/251406)

- Jul 13, 2019 (153)
24 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 13054573 (NC_000019.9:15651316:G:G 251397/251406, NC_000019.9:15651316:G:A 9/251406)
Row 13054574 (NC_000019.9:15651316:G:G 251405/251406, NC_000019.9:15651316:G:T 1/251406)

- Jul 13, 2019 (153)
25 The PAGE Study NC_000019.10 - 15540506 Jul 13, 2019 (153)
26 TopMed NC_000019.10 - 15540506 Oct 12, 2018 (152)
27 ClinVar RCV000000959.2 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
75886050, 3931934, 207154896, ss1362502731, ss1693439202, ss1946529755, ss1959846515, ss2390070384, ss2743740333, ss2750105953, ss2960912777, ss2985134849, ss3021887078, ss3625738025, ss3644718350, ss3652311851, ss3653906721, ss3744164403 NC_000019.9:15651316:G:A NC_000019.10:15540505:G:A (self)
RCV000000959.2, 1223412, 177702954, ss252841400, ss3288912079, ss3725713712, ss3772001943 NC_000019.10:15540505:G:A NC_000019.10:15540505:G:A (self)
ss2743740333 NC_000019.9:15651316:G:T NC_000019.10:15540505:G:T (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 rs118203937
PMID Title Author Year Journal
16436457 Mutations in a new cytochrome P450 gene in lamellar ichthyosis type 3. Lefèvre C et al. 2006 Human molecular genetics

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.post104+4a6ee9c