NM_032237.5:c.565A>G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_032237.5(POMK):āc.565A>Gā(p.Ile189Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000916 in 1,614,238 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_032237.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000841 AC: 128AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00125 AC: 314AN: 250682Hom.: 1 AF XY: 0.00144 AC XY: 195AN XY: 135482
GnomAD4 exome AF: 0.000923 AC: 1349AN: 1461872Hom.: 8 Cov.: 33 AF XY: 0.00101 AC XY: 732AN XY: 727238
GnomAD4 genome AF: 0.000847 AC: 129AN: 152366Hom.: 0 Cov.: 33 AF XY: 0.000792 AC XY: 59AN XY: 74520
ClinVar
Submissions by phenotype
not specified Uncertain:1
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Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12 Uncertain:1
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -
POMK-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). -
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. -
not provided Benign:1
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Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12;C4015184:Limb-girdle muscular dystrophy due to POMK deficiency Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at