16-66966749-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_024922.6(CES3):c.946G>A(p.Val316Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000632 in 1,613,924 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_024922.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CES3 | NM_024922.6 | c.946G>A | p.Val316Ile | missense_variant | 8/13 | ENST00000303334.9 | |
CES3 | NM_001185177.2 | c.946G>A | p.Val316Ile | missense_variant | 8/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CES3 | ENST00000303334.9 | c.946G>A | p.Val316Ile | missense_variant | 8/13 | 1 | NM_024922.6 | P3 | |
CES3 | ENST00000394037.5 | c.946G>A | p.Val316Ile | missense_variant | 8/13 | 1 | A2 | ||
CES3 | ENST00000564715.1 | n.689G>A | non_coding_transcript_exon_variant | 3/3 | 3 | ||||
CES3 | ENST00000570236.1 | c.946G>A | p.Val316Ile | missense_variant, NMD_transcript_variant | 8/11 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000127 AC: 32AN: 251464Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135914
GnomAD4 exome AF: 0.0000670 AC: 98AN: 1461844Hom.: 1 Cov.: 31 AF XY: 0.0000646 AC XY: 47AN XY: 727234
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74282
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 19, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at