rs367543077
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_152490.5(B3GALNT2):c.1423C>T(p.Gln475Ter) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,576 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. Q475Q) has been classified as Likely benign.
Frequency
Consequence
NM_152490.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
B3GALNT2 | NM_152490.5 | c.1423C>T | p.Gln475Ter | stop_gained | 12/12 | ENST00000366600.8 | |
TBCE | NM_003193.5 | c.*1524G>A | 3_prime_UTR_variant | 17/17 | ENST00000642610.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
B3GALNT2 | ENST00000366600.8 | c.1423C>T | p.Gln475Ter | stop_gained | 12/12 | 1 | NM_152490.5 | P1 | |
TBCE | ENST00000642610.2 | c.*1524G>A | 3_prime_UTR_variant | 17/17 | NM_003193.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461576Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727116
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 Pathogenic:1Uncertain:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 07, 2013 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Mar 04, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 41939). This premature translational stop signal has been observed in individual(s) with B3GALNT2-related conditions (PMID: 23453667). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln475*) in the B3GALNT2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 26 amino acid(s) of the B3GALNT2 protein. - |
not provided Other:1
not provided, no classification provided | literature only | Leiden Muscular Dystrophy pages (B3GALNT2) | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at