NM_001136472.2:c.302A>G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM1BP6BS1BS2
The NM_001136472.2(LITAF):āc.302A>Gā(p.Lys101Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000375 in 1,614,136 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001136472.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000247 AC: 62AN: 251232Hom.: 0 AF XY: 0.000258 AC XY: 35AN XY: 135782
GnomAD4 exome AF: 0.000394 AC: 576AN: 1461870Hom.: 0 Cov.: 31 AF XY: 0.000399 AC XY: 290AN XY: 727236
GnomAD4 genome AF: 0.000197 AC: 30AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74454
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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This variant is associated with the following publications: (PMID: 25245565, 26392352, 32376792) -
Charcot-Marie-Tooth disease Uncertain:1
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Charcot-Marie-Tooth disease type 1C Benign:1
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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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at