7-99717214-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_000765.5(CYP3A7):c.484C>T(p.Arg162Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000669 in 1,613,702 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000765.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP3A7 | NM_000765.5 | c.484C>T | p.Arg162Trp | missense_variant | 6/13 | ENST00000336374.4 | |
CYP3A7-CYP3A51P | NM_001256497.3 | c.484C>T | p.Arg162Trp | missense_variant | 6/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP3A7 | ENST00000336374.4 | c.484C>T | p.Arg162Trp | missense_variant | 6/13 | 1 | NM_000765.5 | P1 | |
CYP3A7 | ENST00000477357.5 | n.823C>T | non_coding_transcript_exon_variant | 3/10 | 2 | ||||
CYP3A7 | ENST00000498080.1 | n.52C>T | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152096Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251268Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135790
GnomAD4 exome AF: 0.0000657 AC: 96AN: 1461606Hom.: 0 Cov.: 32 AF XY: 0.0000660 AC XY: 48AN XY: 727098
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152096Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2023 | The c.484C>T (p.R162W) alteration is located in exon 6 (coding exon 6) of the CYP3A7 gene. This alteration results from a C to T substitution at nucleotide position 484, causing the arginine (R) at amino acid position 162 to be replaced by a tryptophan (W). 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