2-42245532-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_019063.5(EML4):c.53C>T(p.Ser18Phe) variant causes a missense change. The variant allele was found at a frequency of 0.000244 in 1,613,370 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_019063.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00107 AC: 162AN: 152074Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000323 AC: 81AN: 250848Hom.: 0 AF XY: 0.000199 AC XY: 27AN XY: 135632
GnomAD4 exome AF: 0.000156 AC: 228AN: 1461178Hom.: 1 Cov.: 30 AF XY: 0.000139 AC XY: 101AN XY: 726898
GnomAD4 genome AF: 0.00109 AC: 166AN: 152192Hom.: 0 Cov.: 31 AF XY: 0.00113 AC XY: 84AN XY: 74408
ClinVar
Submissions by phenotype
EML4-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at