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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.

rs118091316

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr19:15525513 (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.

Alleles
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00653 (820/125568, TOPMED)
T=0.0105 (330/31388, GnomAD)
T=0.0082 (106/13006, GO-ESP) (+ 5 more)
T=0.005 (25/5008, 1000G)
T=0.009 (41/4480, Estonian)
T=0.012 (45/3854, ALSPAC)
T=0.011 (39/3708, TWINSUK)
T=0.01 (9/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CYP4F22 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome
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.p12 chr 19 NC_000019.10:g.15525513C>G
GRCh38.p12 chr 19 NC_000019.10:g.15525513C>T
GRCh37.p13 chr 19 NC_000019.9:g.15636324C>G
GRCh37.p13 chr 19 NC_000019.9:g.15636324C>T
CYP4F22 RefSeqGene NG_007987.1:g.21989C>G
CYP4F22 RefSeqGene NG_007987.1:g.21989C>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.177C>G F [TTC] > L [TTG] Coding Sequence Variant
cytochrome P450 4F22 NP_775754.2:p.Phe59Leu F (Phe) > L (Leu) Missense Variant
CYP4F22 transcript NM_173483.4:c.177C>T F [TTC] > F [TTT] Coding Sequence Variant
cytochrome P450 4F22 NP_775754.2:p.Phe59= F (Phe) > F (Phe) Synonymous Variant
CYP4F22 transcript variant X1 XM_011527692.2:c.177C>G F [TTC] > L [TTG] Coding Sequence Variant
cytochrome P450 4F22 isoform X1 XP_011525994.1:p.Phe59Leu F (Phe) > L (Leu) Missense Variant
CYP4F22 transcript variant X1 XM_011527692.2:c.177C>T F [TTC] > F [TTT] Coding Sequence Variant
cytochrome P450 4F22 isoform X1 XP_011525994.1:p.Phe59= F (Phe) > F (Phe) Synonymous Variant
CYP4F22 transcript variant X2 XM_011527693.2:c.177C>G F [TTC] > L [TTG] Coding Sequence Variant
cytochrome P450 4F22 isoform X1 XP_011525995.1:p.Phe59Leu F (Phe) > L (Leu) Missense Variant
CYP4F22 transcript variant X2 XM_011527693.2:c.177C>T F [TTC] > F [TTT] Coding Sequence Variant
cytochrome P450 4F22 isoform X1 XP_011525995.1:p.Phe59= F (Phe) > F (Phe) Synonymous 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: G (allele ID: 551357 )
ClinVar Accession Disease Names Clinical Significance
RCV000678420.1 Autosomal recessive congenital ichthyosis 5 Pathogenic
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 125568 C=0.99347 T=0.00653
gnomAD - Genomes Global Study-wide 31388 C=0.9895 T=0.0105
gnomAD - Genomes European Sub 18892 C=0.9842 T=0.0158
gnomAD - Genomes African Sub 8710 C=0.999 T=0.001
gnomAD - Genomes East Asian Sub 1560 C=1.000 T=0.000
gnomAD - Genomes Other Sub 1088 C=0.988 T=0.012
gnomAD - Genomes American Sub 848 C=0.99 T=0.01
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=1.00 T=0.00
GO Exome Sequencing Project Global Study-wide 13006 C=0.9918 T=0.0082
GO Exome Sequencing Project European American Sub 8600 C=0.990 T=0.010
GO Exome Sequencing Project African American Sub 4406 C=0.996 T=0.004
1000Genomes Global Study-wide 5008 C=0.995 T=0.005
1000Genomes African Sub 1322 C=1.000 T=0.000
1000Genomes East Asian Sub 1008 C=1.000 T=0.000
1000Genomes Europe Sub 1006 C=0.982 T=0.018
1000Genomes South Asian Sub 978 C=0.99 T=0.01
1000Genomes American Sub 694 C=1.00 T=0.00
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.991 T=0.009
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.988 T=0.012
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.989 T=0.011
Northern Sweden ACPOP Study-wide 600 C=0.98 T=0.01
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 C= G T Note
GRCh38.p12 chr 19 NC_000019.10:g.15...

NC_000019.10:g.15525513=

NC_000019.10:g.15...

NC_000019.10:g.15525513C>G

NC_000019.10:g.15...

NC_000019.10:g.15525513C>T

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

NC_000019.9:g.15636324=

NC_000019.9:g.156...

NC_000019.9:g.15636324C>G

NC_000019.9:g.156...

NC_000019.9:g.15636324C>T

CYP4F22 RefSeqGene NG_007987.1:g.21989= NG_007987.1:g.219...

NG_007987.1:g.21989C>G

NG_007987.1:g.219...

NG_007987.1:g.21989C>T

CYP4F22 transcript NM_173483.3:c.177= NM_173483.3:c.177C>G NM_173483.3:c.177C>T
CYP4F22 transcript NM_173483.4:c.177= NM_173483.4:c.177C>G NM_173483.4:c.177C>T
CYP4F22 transcript variant X1 XM_011527692.2:c....

XM_011527692.2:c.177=

XM_011527692.2:c....

XM_011527692.2:c.177C>G

XM_011527692.2:c....

XM_011527692.2:c.177C>T

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

XM_011527693.2:c.177=

XM_011527693.2:c....

XM_011527693.2:c.177C>G

XM_011527693.2:c....

XM_011527693.2:c.177C>T

cytochrome P450 4F22 NP_775754.2:p.Phe59= NP_775754.2:p.Phe...

NP_775754.2:p.Phe59Leu

NP_775754.2:p.Phe59=
cytochrome P450 4F22 isoform X1 XP_011525994.1:p....

XP_011525994.1:p.Phe59=

XP_011525994.1:p....

XP_011525994.1:p.Phe59Leu

XP_011525994.1:p....

XP_011525994.1:p.Phe59=

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

XP_011525995.1:p.Phe59=

XP_011525995.1:p....

XP_011525995.1:p.Phe59Leu

XP_011525995.1:p....

XP_011525995.1:p.Phe59=

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#.

28 SubSNP, 12 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss237613571 Jul 15, 2010 (132)
2 NHLBI-ESP ss342489143 May 09, 2011 (134)
3 1000GENOMES ss491152527 May 04, 2012 (137)
4 CLINSEQ_SNP ss491760812 May 04, 2012 (137)
5 JMKIDD_LAB ss974504805 Aug 21, 2014 (142)
6 EVA-GONL ss994125727 Aug 21, 2014 (142)
7 1000GENOMES ss1362502328 Aug 21, 2014 (142)
8 EVA_FINRISK ss1584115295 Apr 01, 2015 (144)
9 EVA_UK10K_ALSPAC ss1637635428 Apr 01, 2015 (144)
10 EVA_UK10K_TWINSUK ss1680629461 Apr 01, 2015 (144)
11 EVA_EXAC ss1693439004 Apr 01, 2015 (144)
12 EVA_EXAC ss1693439005 Apr 01, 2015 (144)
13 EVA_DECODE ss1698185372 Apr 01, 2015 (144)
14 EVA_MGP ss1711502229 Apr 01, 2015 (144)
15 WEILL_CORNELL_DGM ss1937611352 Feb 12, 2016 (147)
16 JJLAB ss2029577739 Sep 14, 2016 (149)
17 HUMAN_LONGEVITY ss2224589212 Dec 20, 2016 (150)
18 TOPMED ss2390069479 Dec 20, 2016 (150)
19 GNOMAD ss2743740031 Nov 08, 2017 (151)
20 GNOMAD ss2750105866 Nov 08, 2017 (151)
21 GNOMAD ss2960911643 Nov 08, 2017 (151)
22 SWEGEN ss3017166995 Nov 08, 2017 (151)
23 ILLUMINA ss3021887054 Nov 08, 2017 (151)
24 TOPMED ss3288909531 Nov 08, 2017 (151)
25 ILLUMINA ss3652311823 Oct 12, 2018 (152)
26 EGCUT_WGS ss3683990039 Jul 13, 2019 (153)
27 EVA_DECODE ss3702425802 Jul 13, 2019 (153)
28 ACPOP ss3742888510 Jul 13, 2019 (153)
29 1000Genomes NC_000019.9 - 15636324 Oct 12, 2018 (152)
30 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 15636324 Oct 12, 2018 (152)
31 Genetic variation in the Estonian population NC_000019.9 - 15636324 Oct 12, 2018 (152)
32 ExAC

Submission ignored due to conflicting rows:
Row 3931725 (NC_000019.9:15636323:C:C 119373/120384, NC_000019.9:15636323:C:T 1011/120384)
Row 3931726 (NC_000019.9:15636323:C:C 120383/120384, NC_000019.9:15636323:C:G 1/120384)

- Oct 12, 2018 (152)
33 ExAC

Submission ignored due to conflicting rows:
Row 3931725 (NC_000019.9:15636323:C:C 119373/120384, NC_000019.9:15636323:C:T 1011/120384)
Row 3931726 (NC_000019.9:15636323:C:C 120383/120384, NC_000019.9:15636323:C:G 1/120384)

- Oct 12, 2018 (152)
34 gnomAD - Genomes NC_000019.9 - 15636324 Jul 13, 2019 (153)
35 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 13054254 (NC_000019.9:15636323:C:C 249735/249736, NC_000019.9:15636323:C:G 1/249736)
Row 13054255 (NC_000019.9:15636323:C:C 247639/249736, NC_000019.9:15636323:C:T 2097/249736)

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

Submission ignored due to conflicting rows:
Row 13054254 (NC_000019.9:15636323:C:C 249735/249736, NC_000019.9:15636323:C:G 1/249736)
Row 13054255 (NC_000019.9:15636323:C:C 247639/249736, NC_000019.9:15636323:C:T 2097/249736)

- Jul 13, 2019 (153)
37 GO Exome Sequencing Project NC_000019.9 - 15636324 Oct 12, 2018 (152)
38 Northern Sweden NC_000019.9 - 15636324 Jul 13, 2019 (153)
39 TopMed NC_000019.10 - 15525513 Oct 12, 2018 (152)
40 UK 10K study - Twins NC_000019.9 - 15636324 Oct 12, 2018 (152)
41 ClinVar RCV000678420.1 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
ss1693439005, ss2743740031 NC_000019.9:15636323:C:G NC_000019.10:15525512:C:G (self)
RCV000678420.1 NC_000019.10:15525512:C:G NC_000019.10:15525512:C:G
ss491760812, ss1698185372 NC_000019.8:15497323:C:T NC_000019.10:15525512:C:T (self)
75885633, 42040086, 29728287, 207153777, 1711717, 16173375, 42040086, ss237613571, ss342489143, ss491152527, ss974504805, ss994125727, ss1362502328, ss1584115295, ss1637635428, ss1680629461, ss1693439004, ss1711502229, ss1937611352, ss2029577739, ss2390069479, ss2743740031, ss2750105866, ss2960911643, ss3017166995, ss3021887054, ss3652311823, ss3683990039, ss3742888510 NC_000019.9:15636323:C:T NC_000019.10:15525512:C:T (self)
177700807, ss2224589212, ss3288909531, ss3702425802 NC_000019.10:15525512:C:T NC_000019.10:15525512:C:T (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 rs118091316

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