1-157093050-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001004341.2(ETV3L):c.685G>T(p.Val229Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000285 in 1,404,134 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_001004341.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ETV3L | ENST00000454449.3 | c.685G>T | p.Val229Phe | missense_variant | Exon 5 of 5 | 2 | NM_001004341.2 | ENSP00000430271.1 | ||
ETV3L | ENST00000671886.1 | c.685G>T | p.Val229Phe | missense_variant | Exon 6 of 6 | ENSP00000500322.1 | ||||
ETV3L | ENST00000671942.1 | c.685G>T | p.Val229Phe | missense_variant | Exon 6 of 6 | ENSP00000500028.1 | ||||
ETV3L | ENST00000672100.1 | c.685G>T | p.Val229Phe | missense_variant | Exon 6 of 6 | ENSP00000500154.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000285 AC: 4AN: 1404134Hom.: 0 Cov.: 33 AF XY: 0.00000289 AC XY: 2AN XY: 692960
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
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