chr3-43080871-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6BP7BS1
The NM_032806.6(POMGNT2):c.561C>T(p.His187His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000618 in 1,613,998 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
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.561C>T | p.His187His | synonymous_variant | Exon 2 of 2 | ENST00000344697.3 | NP_116195.2 | |
POMGNT2 | XM_005265515.4 | c.561C>T | p.His187His | synonymous_variant | Exon 3 of 3 | XP_005265572.1 | ||
POMGNT2 | XM_011534163.3 | c.561C>T | p.His187His | synonymous_variant | Exon 3 of 3 | XP_011532465.1 | ||
POMGNT2 | XM_017007353.2 | c.561C>T | p.His187His | synonymous_variant | Exon 4 of 4 | XP_016862842.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000565 AC: 86AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000390 AC: 98AN: 251094Hom.: 0 AF XY: 0.000368 AC XY: 50AN XY: 135736
GnomAD4 exome AF: 0.000623 AC: 911AN: 1461808Hom.: 1 Cov.: 37 AF XY: 0.000583 AC XY: 424AN XY: 727210
GnomAD4 genome AF: 0.000565 AC: 86AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.000619 AC XY: 46AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:2
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8 Benign:1
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not provided Benign:1
POMGNT2: BP4, BP7 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at