chr3-51829705-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001393887.1(IQCF3):c.59G>A(p.Arg20Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 1,613,738 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_001393887.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQCF3 | NM_001393887.1 | c.59G>A | p.Arg20Gln | missense_variant | 2/3 | ENST00000440739.4 | |
IQCF3 | NM_001085479.3 | c.59G>A | p.Arg20Gln | missense_variant | 6/7 | ||
IQCF3 | NM_001207023.2 | c.59G>A | p.Arg20Gln | missense_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQCF3 | ENST00000440739.4 | c.59G>A | p.Arg20Gln | missense_variant | 2/3 | 2 | NM_001393887.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248604Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134896
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461442Hom.: 0 Cov.: 31 AF XY: 0.0000344 AC XY: 25AN XY: 726956
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152296Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74486
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2022 | 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