4-190026440-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001286820.2(FRG2):c.278G>A(p.Arg93Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000476 in 142,992 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R93P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001286820.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000476 AC: 68AN: 142992Hom.: 0 Cov.: 22
GnomAD3 exomes AF: 0.000214 AC: 17AN: 79390Hom.: 0 AF XY: 0.000234 AC XY: 9AN XY: 38450
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000119 AC: 172AN: 1450304Hom.: 4 Cov.: 30 AF XY: 0.000121 AC XY: 87AN XY: 721936
GnomAD4 genome AF: 0.000476 AC: 68AN: 142992Hom.: 0 Cov.: 22 AF XY: 0.000288 AC XY: 20AN XY: 69488
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