3-43080797-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_032806.6(POMGNT2):c.635A>T(p.Lys212Met) variant causes a missense change. The variant allele was found at a frequency of 0.00000616 in 1,461,706 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K212R) has been classified as Uncertain significance.
Frequency
Consequence
NM_032806.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POMGNT2 | NM_032806.6 | c.635A>T | p.Lys212Met | missense_variant | 2/2 | ENST00000344697.3 | |
POMGNT2 | XM_005265515.4 | c.635A>T | p.Lys212Met | missense_variant | 3/3 | ||
POMGNT2 | XM_011534163.3 | c.635A>T | p.Lys212Met | missense_variant | 3/3 | ||
POMGNT2 | XM_017007353.2 | c.635A>T | p.Lys212Met | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POMGNT2 | ENST00000344697.3 | c.635A>T | p.Lys212Met | missense_variant | 2/2 | 1 | NM_032806.6 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250908Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135720
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461706Hom.: 0 Cov.: 37 AF XY: 0.00000688 AC XY: 5AN XY: 727164
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at