3-197943981-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_032263.5(IQCG):c.79G>A(p.Glu27Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000203 in 1,613,900 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_032263.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQCG | NM_032263.5 | c.79G>A | p.Glu27Lys | missense_variant | 4/12 | ENST00000265239.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQCG | ENST00000265239.11 | c.79G>A | p.Glu27Lys | missense_variant | 4/12 | 1 | NM_032263.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000197 AC: 30AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000131 AC: 33AN: 251288Hom.: 1 AF XY: 0.000147 AC XY: 20AN XY: 135842
GnomAD4 exome AF: 0.000203 AC: 297AN: 1461798Hom.: 2 Cov.: 32 AF XY: 0.000219 AC XY: 159AN XY: 727206
GnomAD4 genome ? AF: 0.000197 AC: 30AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74308
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 06, 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