rs113361507
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_032237.5(POMK):c.1006G>A(p.Asp336Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000939 in 1,613,846 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_032237.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POMK | NM_032237.5 | c.1006G>A | p.Asp336Asn | missense_variant | 5/5 | ENST00000331373.10 | |
POMK | NM_001277971.2 | c.1006G>A | p.Asp336Asn | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POMK | ENST00000331373.10 | c.1006G>A | p.Asp336Asn | missense_variant | 5/5 | 2 | NM_032237.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00248 AC: 378AN: 152136Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00169 AC: 423AN: 250672Hom.: 7 AF XY: 0.00185 AC XY: 251AN XY: 135612
GnomAD4 exome AF: 0.000775 AC: 1133AN: 1461592Hom.: 16 Cov.: 33 AF XY: 0.000975 AC XY: 709AN XY: 727104
GnomAD4 genome ? AF: 0.00252 AC: 383AN: 152254Hom.: 2 Cov.: 33 AF XY: 0.00262 AC XY: 195AN XY: 74434
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 22, 2019 | - - |
POMK-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 26, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 28, 2021 | - - |
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12;C4015184:Limb-girdle muscular dystrophy due to POMK deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at