rs201333414
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 4P and 10B. PM1PM2BP4_StrongBP6_ModerateBS1
The NM_032806.6(POMGNT2):c.499G>A(p.Val167Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000923 in 1,614,116 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_032806.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POMGNT2 | NM_032806.6 | c.499G>A | p.Val167Ile | missense_variant | 2/2 | ENST00000344697.3 | |
POMGNT2 | XM_005265515.4 | c.499G>A | p.Val167Ile | missense_variant | 3/3 | ||
POMGNT2 | XM_011534163.3 | c.499G>A | p.Val167Ile | missense_variant | 3/3 | ||
POMGNT2 | XM_017007353.2 | c.499G>A | p.Val167Ile | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POMGNT2 | ENST00000344697.3 | c.499G>A | p.Val167Ile | missense_variant | 2/2 | 1 | NM_032806.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152140Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000187 AC: 47AN: 251324Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135850
GnomAD4 exome AF: 0.0000910 AC: 133AN: 1461858Hom.: 0 Cov.: 37 AF XY: 0.0000866 AC XY: 63AN XY: 727224
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74446
ClinVar
Submissions by phenotype
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at