chr19-40845449-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_000762.6(CYP2A6):c.1006G>A(p.Gly336Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000304 in 1,611,610 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000762.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP2A6 | ENST00000301141.10 | c.1006G>A | p.Gly336Ser | missense_variant | Exon 7 of 9 | 1 | NM_000762.6 | ENSP00000301141.4 | ||
CYP2A6 | ENST00000596719.5 | n.857G>A | non_coding_transcript_exon_variant | Exon 6 of 6 | 1 | |||||
ENSG00000268797 | ENST00000601627.1 | n.117+44034C>T | intron_variant | Intron 1 of 3 | 3 | ENSP00000469533.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151336Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251124Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135742
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1460274Hom.: 0 Cov.: 32 AF XY: 0.0000358 AC XY: 26AN XY: 726444
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151336Hom.: 0 Cov.: 31 AF XY: 0.0000271 AC XY: 2AN XY: 73812
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1006G>A (p.G336S) alteration is located in exon 7 (coding exon 7) of the CYP2A6 gene. This alteration results from a G to A substitution at nucleotide position 1006, causing the glycine (G) at amino acid position 336 to be replaced by a serine (S). 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