rs28399463
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000762.6(CYP2A6):āc.1252A>Gā(p.Asn418Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00125 in 1,610,716 control chromosomes in the GnomAD database, including 67 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). 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 -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2A6 | NM_000762.6 | c.1252A>G | p.Asn418Asp | missense_variant | 8/9 | ENST00000301141.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2A6 | ENST00000301141.10 | c.1252A>G | p.Asn418Asp | missense_variant | 8/9 | 1 | NM_000762.6 | P1 | |
CYP2A6 | ENST00000599960.1 | n.171A>G | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00728 AC: 1102AN: 151270Hom.: 33 Cov.: 31
GnomAD3 exomes AF: 0.000962 AC: 241AN: 250628Hom.: 14 AF XY: 0.000693 AC XY: 94AN XY: 135550
GnomAD4 exome AF: 0.000619 AC: 904AN: 1459330Hom.: 34 Cov.: 32 AF XY: 0.000529 AC XY: 384AN XY: 726040
GnomAD4 genome ? AF: 0.00728 AC: 1102AN: 151386Hom.: 33 Cov.: 31 AF XY: 0.00729 AC XY: 539AN XY: 73954
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at