10-94946177-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000771.4(CYP2C9):​c.482-1602A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,050 control chromosomes in the GnomAD database, including 22,819 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.54 ( 22819 hom., cov: 32)

Consequence

CYP2C9
NM_000771.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.881
Variant links:
Genes affected
CYP2C9 (HGNC:2623): (cytochrome P450 family 2 subfamily C member 9) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum and its expression is induced by rifampin. The enzyme is known to metabolize many xenobiotics, including phenytoin, tolbutamide, ibuprofen and S-warfarin. Studies identifying individuals who are poor metabolizers of phenytoin and tolbutamide suggest that this gene is polymorphic. The gene is located within a cluster of cytochrome P450 genes on chromosome 10q24. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CYP2C9NM_000771.4 linkc.482-1602A>G intron_variant Intron 3 of 8 ENST00000260682.8 NP_000762.2 P11712-1S5RV20

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CYP2C9ENST00000260682.8 linkc.482-1602A>G intron_variant Intron 3 of 8 1 NM_000771.4 ENSP00000260682.6 P11712-1
CYP2C9ENST00000473496.1 linkn.253-1602A>G intron_variant Intron 2 of 3 2
CYP2C9ENST00000643112.1 linkn.482-1602A>G intron_variant Intron 3 of 7 ENSP00000496202.1 A0A2R8YF67
CYP2C9ENST00000645207.1 linkn.635-1602A>G intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
AF:
0.539
AC:
81825
AN:
151932
Hom.:
22799
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.655
Gnomad AMI
AF:
0.616
Gnomad AMR
AF:
0.400
Gnomad ASJ
AF:
0.499
Gnomad EAS
AF:
0.376
Gnomad SAS
AF:
0.527
Gnomad FIN
AF:
0.513
Gnomad MID
AF:
0.487
Gnomad NFE
AF:
0.518
Gnomad OTH
AF:
0.516
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.539
AC:
81886
AN:
152050
Hom.:
22819
Cov.:
32
AF XY:
0.536
AC XY:
39812
AN XY:
74316
show subpopulations
Gnomad4 AFR
AF:
0.654
Gnomad4 AMR
AF:
0.400
Gnomad4 ASJ
AF:
0.499
Gnomad4 EAS
AF:
0.375
Gnomad4 SAS
AF:
0.527
Gnomad4 FIN
AF:
0.513
Gnomad4 NFE
AF:
0.518
Gnomad4 OTH
AF:
0.520
Alfa
AF:
0.535
Hom.:
2698
Bravo
AF:
0.532

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.44
DANN
Benign
0.37

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6583964; hg19: chr10-96705934; API