1-235480130-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_152490.5(B3GALNT2):c.575G>A(p.Arg192His) variant causes a missense change. The variant allele was found at a frequency of 0.000598 in 1,613,508 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R192C) has been classified as Uncertain significance.
Frequency
Consequence
NM_152490.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 42AN: 152028Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000582 AC: 146AN: 250938Hom.: 2 AF XY: 0.000531 AC XY: 72AN XY: 135622
GnomAD4 exome AF: 0.000632 AC: 923AN: 1461480Hom.: 3 Cov.: 30 AF XY: 0.000594 AC XY: 432AN XY: 727056
GnomAD4 genome AF: 0.000276 AC: 42AN: 152028Hom.: 0 Cov.: 31 AF XY: 0.000269 AC XY: 20AN XY: 74234
ClinVar
Submissions by phenotype
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 15, 2025 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Oct 15, 2019 | - - |
not provided Benign:1Other:1
not provided, no classification provided | phenotyping only | GenomeConnect - Invitae Patient Insights Network | - | Variant interpreted as Benign and reported on 09-08-2020 by Lab Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 07, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at