chr3-43081420-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6BP7BS1
The NM_032806.6(POMGNT2):c.12G>A(p.Ser4Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,571,152 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). Synonymous variant affecting the same amino acid position (i.e. S4S) has been classified as Likely benign.
Frequency
Consequence
NM_032806.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POMGNT2 | NM_032806.6 | c.12G>A | p.Ser4Ser | synonymous_variant | Exon 2 of 2 | ENST00000344697.3 | NP_116195.2 | |
POMGNT2 | XM_005265515.4 | c.12G>A | p.Ser4Ser | synonymous_variant | Exon 3 of 3 | XP_005265572.1 | ||
POMGNT2 | XM_011534163.3 | c.12G>A | p.Ser4Ser | synonymous_variant | Exon 3 of 3 | XP_011532465.1 | ||
POMGNT2 | XM_017007353.2 | c.12G>A | p.Ser4Ser | synonymous_variant | Exon 4 of 4 | XP_016862842.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000176 AC: 36AN: 204806Hom.: 0 AF XY: 0.000190 AC XY: 21AN XY: 110286
GnomAD4 exome AF: 0.000108 AC: 153AN: 1418846Hom.: 0 Cov.: 37 AF XY: 0.000127 AC XY: 89AN XY: 701790
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152306Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
- -
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8 Benign:1
- -
not provided Benign:1
POMGNT2: BP4, BP7 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at