chr15-74720644-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001319217.2(CYP1A1):c.1384A>G(p.Ile462Val) variant causes a missense change. The variant allele was found at a frequency of 0.0564 in 1,613,998 control chromosomes in the GnomAD database, including 6,819 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001319217.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP1A1 | NM_001319217.2 | c.1384A>G | p.Ile462Val | missense_variant | 7/7 | ENST00000379727.8 | |
CYP1A1 | NM_000499.5 | c.1384A>G | p.Ile462Val | missense_variant | 7/7 | ||
CYP1A1 | NM_001319216.2 | c.1297A>G | p.Ile433Val | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP1A1 | ENST00000379727.8 | c.1384A>G | p.Ile462Val | missense_variant | 7/7 | 1 | NM_001319217.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0634 AC: 9646AN: 152082Hom.: 868 Cov.: 32
GnomAD3 exomes AF: 0.108 AC: 27169AN: 251354Hom.: 3595 AF XY: 0.101 AC XY: 13702AN XY: 135850
GnomAD4 exome AF: 0.0556 AC: 81313AN: 1461798Hom.: 5945 Cov.: 31 AF XY: 0.0565 AC XY: 41084AN XY: 727208
GnomAD4 genome ? AF: 0.0634 AC: 9657AN: 152200Hom.: 874 Cov.: 32 AF XY: 0.0697 AC XY: 5185AN XY: 74412
ClinVar
Submissions by phenotype
CYP1A1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 18, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at