chr16-66963910-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_024922.6(CES3):c.535C>T(p.Arg179Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000348 in 1,613,450 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R179H) has been classified as Likely benign.
Frequency
Consequence
NM_024922.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CES3 | NM_024922.6 | c.535C>T | p.Arg179Cys | missense_variant | 4/13 | ENST00000303334.9 | |
CES3 | NM_001185177.2 | c.535C>T | p.Arg179Cys | missense_variant | 4/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CES3 | ENST00000303334.9 | c.535C>T | p.Arg179Cys | missense_variant | 4/13 | 1 | NM_024922.6 | P3 | |
CES3 | ENST00000394037.5 | c.535C>T | p.Arg179Cys | missense_variant | 4/13 | 1 | A2 | ||
CES3 | ENST00000570236.1 | c.535C>T | p.Arg179Cys | missense_variant, NMD_transcript_variant | 4/11 | 5 | |||
CES3 | ENST00000566453.1 | c.*431C>T | 3_prime_UTR_variant, NMD_transcript_variant | 5/7 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000361 AC: 55AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000282 AC: 71AN: 251392Hom.: 0 AF XY: 0.000353 AC XY: 48AN XY: 135858
GnomAD4 exome AF: 0.000346 AC: 506AN: 1461136Hom.: 0 Cov.: 32 AF XY: 0.000348 AC XY: 253AN XY: 726734
GnomAD4 genome AF: 0.000361 AC: 55AN: 152314Hom.: 0 Cov.: 33 AF XY: 0.000457 AC XY: 34AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 07, 2024 | The c.535C>T (p.R179C) alteration is located in exon 4 (coding exon 4) of the CES3 gene. This alteration results from a C to T substitution at nucleotide position 535, causing the arginine (R) at amino acid position 179 to be replaced by a cysteine (C). 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