4-190025763-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.638G>A(p.Arg213Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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. R213W) 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
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FRG2 | ENST00000504750.6 | c.638G>A | p.Arg213Gln | missense_variant | Exon 4 of 4 | 1 | NM_001286820.2 | ENSP00000424015.1 | ||
FRG2 | ENST00000378763.1 | c.635G>A | p.Arg212Gln | missense_variant | Exon 4 of 4 | 1 | ENSP00000368039.1 |
Frequencies
GnomAD3 genomes AF: 0.000107 AC: 16AN: 148978Hom.: 0 Cov.: 22
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000548 AC: 80AN: 1460686Hom.: 0 Cov.: 31 AF XY: 0.0000578 AC XY: 42AN XY: 726506
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000114 AC: 17AN: 149082Hom.: 0 Cov.: 22 AF XY: 0.0000689 AC XY: 5AN XY: 72576
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