chr3-43080048-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_032806.6(POMGNT2):c.1384C>T(p.Arg462Trp) variant causes a missense change. The variant allele was found at a frequency of 0.00131 in 1,613,824 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R462L) has been classified as Likely benign.
Frequency
Consequence
NM_032806.6 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 |
---|---|---|---|---|---|---|---|
POMGNT2 | NM_032806.6 | c.1384C>T | p.Arg462Trp | missense_variant | 2/2 | ENST00000344697.3 | |
POMGNT2 | XM_005265515.4 | c.1384C>T | p.Arg462Trp | missense_variant | 3/3 | ||
POMGNT2 | XM_011534163.3 | c.1384C>T | p.Arg462Trp | missense_variant | 3/3 | ||
POMGNT2 | XM_017007353.2 | c.1384C>T | p.Arg462Trp | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POMGNT2 | ENST00000344697.3 | c.1384C>T | p.Arg462Trp | missense_variant | 2/2 | 1 | NM_032806.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00706 AC: 1074AN: 152224Hom.: 14 Cov.: 33
GnomAD3 exomes AF: 0.00172 AC: 432AN: 250790Hom.: 3 AF XY: 0.00141 AC XY: 191AN XY: 135624
GnomAD4 exome AF: 0.000708 AC: 1035AN: 1461482Hom.: 11 Cov.: 29 AF XY: 0.000615 AC XY: 447AN XY: 727050
GnomAD4 genome AF: 0.00706 AC: 1076AN: 152342Hom.: 14 Cov.: 33 AF XY: 0.00705 AC XY: 525AN XY: 74492
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Feb 07, 2017 | - - |
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 27, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at