7-2572254-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_152558.5(IQCE):c.322G>A(p.Gly108Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000824 in 1,613,988 control chromosomes in the GnomAD database, including 1 homozygotes. 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_152558.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IQCE | NM_152558.5 | c.322G>A | p.Gly108Ser | missense_variant | 5/22 | ENST00000402050.7 | NP_689771.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IQCE | ENST00000402050.7 | c.322G>A | p.Gly108Ser | missense_variant | 5/22 | 1 | NM_152558.5 | ENSP00000385597.2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000160 AC: 40AN: 249516Hom.: 0 AF XY: 0.000163 AC XY: 22AN XY: 135378
GnomAD4 exome AF: 0.0000835 AC: 122AN: 1461784Hom.: 1 Cov.: 33 AF XY: 0.0000990 AC XY: 72AN XY: 727198
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74364
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 17, 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