chr10-95064934-G-A
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_000770.3(CYP2C8):c.508C>T(p.Leu170=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000173 in 1,589,826 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00016 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00017 ( 0 hom. )
Consequence
CYP2C8
NM_000770.3 synonymous
NM_000770.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.385
Genes affected
CYP2C8 (HGNC:2622): (cytochrome P450 family 2 subfamily C member 8) 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 phenobarbital. The enzyme is known to metabolize many xenobiotics, including the anticonvulsive drug mephenytoin, benzo(a)pyrene, 7-ethyoxycoumarin, and the anti-cancer drug taxol. This gene is located within a cluster of cytochrome P450 genes on chromosome 10q24. Several transcript variants encoding a few different isoforms have been found for this gene. [provided by RefSeq, Nov 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
Variant 10-95064934-G-A is Benign according to our data. Variant chr10-95064934-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2640707.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.385 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2C8 | NM_000770.3 | c.508C>T | p.Leu170= | synonymous_variant | 4/9 | ENST00000371270.6 | |
CYP2C8 | NM_001198853.1 | c.298C>T | p.Leu100= | synonymous_variant | 4/9 | ||
CYP2C8 | NM_001198855.1 | c.298C>T | p.Leu100= | synonymous_variant | 5/10 | ||
CYP2C8 | NM_001198854.1 | c.202C>T | p.Leu68= | synonymous_variant | 3/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2C8 | ENST00000371270.6 | c.508C>T | p.Leu170= | synonymous_variant | 4/9 | 1 | NM_000770.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 151970Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000184 AC: 45AN: 243950Hom.: 0 AF XY: 0.000220 AC XY: 29AN XY: 132018
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GnomAD4 exome AF: 0.000175 AC: 251AN: 1437856Hom.: 0 Cov.: 31 AF XY: 0.000160 AC XY: 114AN XY: 714246
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GnomAD4 genome AF: 0.000158 AC: 24AN: 151970Hom.: 0 Cov.: 32 AF XY: 0.000229 AC XY: 17AN XY: 74210
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2022 | CYP2C8: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at