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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
chr19:15549170 (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.

Variation Type
SNV Single Nucleotide Variation
T=0.00006 (14/251446, GnomAD_exome)
T=0.00008 (10/125568, TOPMED)
T=0.00007 (8/121322, ExAC) (+ 2 more)
T=0.0001 (9/78696, PAGE_STUDY)
T=0.0000 (1/31342, GnomAD)
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.15549170C>T
GRCh37.p13 chr 19 NC_000019.9:g.15659981C>T
CYP4F22 RefSeqGene NG_007987.1:g.45646C>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.1303C>T H [CAC] > Y [TAC] Coding Sequence Variant
cytochrome P450 4F22 NP_775754.2:p.His435Tyr H (His) > Y (Tyr) Missense Variant
CYP4F22 transcript variant X1 XM_011527692.2:c.1303C>T H [CAC] > Y [TAC] Coding Sequence Variant
cytochrome P450 4F22 isoform X1 XP_011525994.1:p.His435Tyr H (His) > Y (Tyr) Missense Variant
CYP4F22 transcript variant X2 XM_011527693.2:c.1303C>T H [CAC] > Y [TAC] Coding Sequence Variant
cytochrome P450 4F22 isoform X1 XP_011525995.1:p.His435Tyr H (His) > Y (Tyr) 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: T (allele ID: 15948 )
ClinVar Accession Disease Names Clinical Significance
RCV000000957.2 Autosomal recessive congenital ichthyosis 5 Pathogenic
RCV000412942.1 not provided 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 251446 C=0.99994 T=0.00006
gnomAD - Exomes European Sub 135392 C=0.99993 T=0.00007
gnomAD - Exomes Asian Sub 49010 C=1.0000 T=0.0000
gnomAD - Exomes American Sub 34576 C=0.9999 T=0.0001
gnomAD - Exomes African Sub 16254 C=1.0000 T=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 10078 C=1.0000 T=0.0000
gnomAD - Exomes Other Sub 6136 C=1.000 T=0.000
TopMed Global Study-wide 125568 C=0.99992 T=0.00008
ExAC Global Study-wide 121322 C=0.99993 T=0.00007
ExAC Europe Sub 73296 C=0.9999 T=0.0001
ExAC Asian Sub 25164 C=1.0000 T=0.0000
ExAC American Sub 11570 C=0.9999 T=0.0001
ExAC African Sub 10384 C=1.0000 T=0.0000
ExAC Other Sub 908 C=1.00 T=0.00
The PAGE Study Global Study-wide 78696 C=0.9999 T=0.0001
The PAGE Study AfricanAmerican Sub 32514 C=0.9999 T=0.0001
The PAGE Study Mexican Sub 10808 C=0.9996 T=0.0004
The PAGE Study Asian Sub 8318 C=1.000 T=0.000
The PAGE Study PuertoRican Sub 7918 C=1.000 T=0.000
The PAGE Study NativeHawaiian Sub 4532 C=1.000 T=0.000
The PAGE Study Cuban Sub 4230 C=1.000 T=0.000
The PAGE Study Dominican Sub 3828 C=1.000 T=0.000
The PAGE Study CentralAmerican Sub 2450 C=1.000 T=0.000
The PAGE Study SouthAmerican Sub 1982 C=0.999 T=0.001
The PAGE Study NativeAmerican Sub 1260 C=1.000 T=0.000
The PAGE Study SouthAsian Sub 856 C=1.00 T=0.00
gnomAD - Genomes Global Study-wide 31342 C=1.0000 T=0.0000
gnomAD - Genomes European Sub 18868 C=0.9999 T=0.0001
gnomAD - Genomes African Sub 8694 C=1.000 T=0.000
gnomAD - Genomes East Asian Sub 1554 C=1.000 T=0.000
gnomAD - Genomes Other Sub 1088 C=1.000 T=0.000
gnomAD - Genomes American Sub 848 C=1.00 T=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=1.00 T=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 C= T Note
GRCh38.p12 chr 19 NC_000019.10:g.15549170= NC_000019.10:g.15549170C>T
GRCh37.p13 chr 19 NC_000019.9:g.15659981= NC_000019.9:g.15659981C>T
CYP4F22 RefSeqGene NG_007987.1:g.45646= NG_007987.1:g.45646C>T
CYP4F22 transcript NM_173483.3:c.1303= NM_173483.3:c.1303C>T
CYP4F22 transcript NM_173483.4:c.1303= NM_173483.4:c.1303C>T
CYP4F22 transcript variant X1 XM_011527692.2:c.1303= XM_011527692.2:c.1303C>T
CYP4F22 transcript variant X2 XM_011527693.2:c.1303= XM_011527693.2:c.1303C>T
cytochrome P450 4F22 NP_775754.2:p.His435= NP_775754.2:p.His435Tyr
cytochrome P450 4F22 isoform X1 XP_011525994.1:p.His435= XP_011525994.1:p.His435Tyr
cytochrome P450 4F22 isoform X1 XP_011525995.1:p.His435= XP_011525995.1:p.His435Tyr

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#.

13 SubSNP, 5 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss252841398 Aug 10, 2010 (132)
2 EVA_EXAC ss1693439385 Apr 01, 2015 (144)
3 EVA_MGP ss1711502251 Apr 01, 2015 (144)
4 ILLUMINA ss1959846538 Feb 12, 2016 (147)
5 TOPMED ss2390070944 Dec 20, 2016 (150)
6 GNOMAD ss2743740588 Nov 08, 2017 (151)
7 GNOMAD ss2750106044 Nov 08, 2017 (151)
8 GNOMAD ss2960913546 Nov 08, 2017 (151)
9 ILLUMINA ss3021887098 Nov 08, 2017 (151)
10 TOPMED ss3288913933 Nov 08, 2017 (151)
11 ILLUMINA ss3652311872 Oct 12, 2018 (152)
12 ILLUMINA ss3725713732 Jul 13, 2019 (153)
13 PAGE_CC ss3772001962 Jul 13, 2019 (153)
14 ExAC NC_000019.9 - 15659981 Oct 12, 2018 (152)
15 gnomAD - Genomes NC_000019.9 - 15659981 Jul 13, 2019 (153)
16 gnomAD - Exomes NC_000019.9 - 15659981 Jul 13, 2019 (153)
17 The PAGE Study NC_000019.10 - 15549170 Jul 13, 2019 (153)
18 TopMed NC_000019.10 - 15549170 Oct 12, 2018 (152)
19 ClinVar RCV000000957.2 Oct 12, 2018 (152)
20 ClinVar RCV000412942.1 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
3932154, 207155683, 13054865, ss1693439385, ss1711502251, ss1959846538, ss2390070944, ss2743740588, ss2750106044, ss2960913546, ss3021887098, ss3652311872 NC_000019.9:15659980:C:T NC_000019.10:15549169:C:T (self)
RCV000000957.2, RCV000412942.1, 1223431, 177704281, ss252841398, ss3288913933, ss3725713732, ss3772001962 NC_000019.10:15549169:C:T NC_000019.10:15549169:C: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 rs118203935
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