chr16-66969745-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024922.6(CES3):c.1129G>A(p.Val377Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000159 in 1,612,154 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
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.1129G>A | p.Val377Ile | missense_variant | 9/13 | ENST00000303334.9 | |
CES3 | NM_001185177.2 | c.1129G>A | p.Val377Ile | missense_variant | 9/13 | ||
CES3 | NM_001185176.2 | c.46G>A | p.Val16Ile | missense_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CES3 | ENST00000303334.9 | c.1129G>A | p.Val377Ile | missense_variant | 9/13 | 1 | NM_024922.6 | P3 | |
CES3 | ENST00000394037.5 | c.1129G>A | p.Val377Ile | missense_variant | 9/13 | 1 | A2 | ||
CES3 | ENST00000543856.1 | c.46G>A | p.Val16Ile | missense_variant | 2/6 | 2 | |||
CES3 | ENST00000570236.1 | c.1063-2611G>A | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000771 AC: 19AN: 246474Hom.: 0 AF XY: 0.0000600 AC XY: 8AN XY: 133314
GnomAD4 exome AF: 0.000167 AC: 244AN: 1459996Hom.: 0 Cov.: 30 AF XY: 0.000160 AC XY: 116AN XY: 726148
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 30, 2022 | The c.1129G>A (p.V377I) alteration is located in exon 9 (coding exon 9) of the CES3 gene. This alteration results from a G to A substitution at nucleotide position 1129, causing the valine (V) at amino acid position 377 to be replaced by an isoleucine (I). 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