14-104701402-G-A
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_022489.4(INF2):c.37G>A(p.Ala13Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000355 in 1,593,462 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_022489.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000309 AC: 47AN: 152266Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000357 AC: 76AN: 212926Hom.: 1 AF XY: 0.000344 AC XY: 40AN XY: 116412
GnomAD4 exome AF: 0.000360 AC: 519AN: 1441078Hom.: 1 Cov.: 31 AF XY: 0.000376 AC XY: 269AN XY: 714884
GnomAD4 genome AF: 0.000308 AC: 47AN: 152384Hom.: 1 Cov.: 33 AF XY: 0.000242 AC XY: 18AN XY: 74516
ClinVar
Submissions by phenotype
not provided Benign:4
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In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 23014460, 20023659, 30295827) -
INF2: PP2, BS1 -
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Focal segmental glomerulosclerosis 5;C4302667:Charcot-Marie-Tooth disease dominant intermediate E Benign:1
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Focal segmental glomerulosclerosis 5 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Inborn genetic diseases 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. -
INF2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at