rs111033610
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_000762.6(CYP2A6):āc.670T>Cā(p.Ser224Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00043 in 1,611,718 control chromosomes in the GnomAD database, including 75 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as drug response (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000762.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2A6 | NM_000762.6 | c.670T>C | p.Ser224Pro | missense_variant | 5/9 | ENST00000301141.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2A6 | ENST00000301141.10 | c.670T>C | p.Ser224Pro | missense_variant | 5/9 | 1 | NM_000762.6 | P1 | |
CYP2A6 | ENST00000596719.5 | n.521T>C | non_coding_transcript_exon_variant | 4/6 | 1 | ||||
CYP2A6 | ENST00000600495.1 | c.*482T>C | 3_prime_UTR_variant, NMD_transcript_variant | 5/6 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000389 AC: 59AN: 151688Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00109 AC: 272AN: 249718Hom.: 21 AF XY: 0.00104 AC XY: 140AN XY: 134984
GnomAD4 exome AF: 0.000434 AC: 634AN: 1459916Hom.: 73 Cov.: 31 AF XY: 0.000472 AC XY: 343AN XY: 726268
GnomAD4 genome ? AF: 0.000389 AC: 59AN: 151802Hom.: 2 Cov.: 32 AF XY: 0.000458 AC XY: 34AN XY: 74176
ClinVar
Submissions by phenotype
Tegafur response Other:1
drug response, no assertion criteria provided | literature only | OMIM | Jun 01, 2002 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at