chr16-55826265-T-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001025195.2(CES1):c.291A>T(p.Leu97Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000564 in 1,613,900 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001025195.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CES1 | NM_001025195.2 | c.291A>T | p.Leu97Phe | missense_variant | 3/14 | ENST00000360526.8 | |
CES1 | NM_001025194.2 | c.288A>T | p.Leu96Phe | missense_variant | 3/14 | ||
CES1 | NM_001266.5 | c.288A>T | p.Leu96Phe | missense_variant | 3/14 | ||
CES1 | XM_005255774.3 | c.291A>T | p.Leu97Phe | missense_variant | 3/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CES1 | ENST00000360526.8 | c.291A>T | p.Leu97Phe | missense_variant | 3/14 | 1 | NM_001025195.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000204 AC: 31AN: 152122Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251176Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135740
GnomAD4 exome AF: 0.0000410 AC: 60AN: 1461660Hom.: 0 Cov.: 32 AF XY: 0.0000371 AC XY: 27AN XY: 727136
GnomAD4 genome ? AF: 0.000204 AC: 31AN: 152240Hom.: 0 Cov.: 33 AF XY: 0.000228 AC XY: 17AN XY: 74452
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 05, 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