chr15-74751198-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000761.5(CYP1A2):c.841C>T(p.Arg281Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00149 in 1,613,996 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000761.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP1A2 | NM_000761.5 | c.841C>T | p.Arg281Trp | missense_variant | 3/7 | ENST00000343932.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP1A2 | ENST00000343932.5 | c.841C>T | p.Arg281Trp | missense_variant | 3/7 | 1 | NM_000761.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000986 AC: 150AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00118 AC: 297AN: 251104Hom.: 0 AF XY: 0.00125 AC XY: 169AN XY: 135708
GnomAD4 exome AF: 0.00154 AC: 2254AN: 1461778Hom.: 1 Cov.: 31 AF XY: 0.00150 AC XY: 1092AN XY: 727208
GnomAD4 genome ? AF: 0.000985 AC: 150AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.00102 AC XY: 76AN XY: 74420
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 10, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at