15-74722964-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001319217.2(CYP1A1):c.134G>A(p.Gly45Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00453 in 1,614,170 control chromosomes in the GnomAD database, including 529 homozygotes. In-silico tool predicts 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.134G>A | p.Gly45Asp | missense_variant | 2/7 | ENST00000379727.8 | |
CYP1A1 | NM_000499.5 | c.134G>A | p.Gly45Asp | missense_variant | 2/7 | ||
CYP1A1 | NM_001319216.2 | c.134G>A | p.Gly45Asp | missense_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP1A1 | ENST00000379727.8 | c.134G>A | p.Gly45Asp | missense_variant | 2/7 | 1 | NM_001319217.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00494 AC: 751AN: 152174Hom.: 53 Cov.: 32
GnomAD3 exomes AF: 0.0108 AC: 2707AN: 251386Hom.: 188 AF XY: 0.0100 AC XY: 1360AN XY: 135888
GnomAD4 exome AF: 0.00448 AC: 6555AN: 1461878Hom.: 476 Cov.: 31 AF XY: 0.00433 AC XY: 3147AN XY: 727234
GnomAD4 genome AF: 0.00494 AC: 752AN: 152292Hom.: 53 Cov.: 32 AF XY: 0.00571 AC XY: 425AN XY: 74458
ClinVar
Submissions by phenotype
CYP1A1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 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