chr19-40848635-C-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_000762.6(CYP2A6):c.472G>T(p.Asp158Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000931 in 1,611,704 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D158E) has been classified as Likely benign.
Frequency
Consequence
NM_000762.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2A6 | NM_000762.6 | c.472G>T | p.Asp158Tyr | missense_variant | 3/9 | ENST00000301141.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2A6 | ENST00000301141.10 | c.472G>T | p.Asp158Tyr | missense_variant | 3/9 | 1 | NM_000762.6 | P1 | |
CYP2A6 | ENST00000596719.5 | n.323G>T | non_coding_transcript_exon_variant | 2/6 | 1 | ||||
CYP2A6 | ENST00000600495.1 | c.*284G>T | 3_prime_UTR_variant, NMD_transcript_variant | 3/6 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151628Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000800 AC: 2AN: 250096Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135436
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1460076Hom.: 0 Cov.: 64 AF XY: 0.00000688 AC XY: 5AN XY: 726350
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151628Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 73974
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 07, 2023 | The c.472G>T (p.D158Y) alteration is located in exon 3 (coding exon 3) of the CYP2A6 gene. This alteration results from a G to T substitution at nucleotide position 472, causing the aspartic acid (D) at amino acid position 158 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at