NM_001111125.3:c.477G>A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001111125.3(IQSEC2):c.477G>A(p.Leu159Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00387 in 1,162,443 control chromosomes in the GnomAD database, including 105 homozygotes. There are 1,276 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001111125.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0207 AC: 2324AN: 112334Hom.: 50 Cov.: 23 AF XY: 0.0193 AC XY: 667AN XY: 34590
GnomAD3 exomes AF: 0.00459 AC: 476AN: 103729Hom.: 13 AF XY: 0.00331 AC XY: 119AN XY: 35987
GnomAD4 exome AF: 0.00207 AC: 2172AN: 1050058Hom.: 55 Cov.: 32 AF XY: 0.00177 AC XY: 605AN XY: 342216
GnomAD4 genome AF: 0.0207 AC: 2329AN: 112385Hom.: 50 Cov.: 23 AF XY: 0.0194 AC XY: 671AN XY: 34651
ClinVar
Submissions by phenotype
not specified Benign:3
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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Inborn genetic diseases Benign:1
This alteration is classified as 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. -
Intellectual disability, X-linked 1 Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at