chr19-17808232-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_014256.4(B3GNT3):c.425G>A(p.Arg142His) variant causes a missense change. The variant allele was found at a frequency of 0.00000205 in 1,461,218 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 (★).
Frequency
Consequence
NM_014256.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
B3GNT3 | NM_014256.4 | c.425G>A | p.Arg142His | missense_variant | Exon 2 of 3 | ENST00000318683.7 | NP_055071.2 | |
B3GNT3 | XM_011527626.3 | c.425G>A | p.Arg142His | missense_variant | Exon 2 of 3 | XP_011525928.1 | ||
B3GNT3 | XM_047438042.1 | c.425G>A | p.Arg142His | missense_variant | Exon 2 of 3 | XP_047293998.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
B3GNT3 | ENST00000318683.7 | c.425G>A | p.Arg142His | missense_variant | Exon 2 of 3 | 1 | NM_014256.4 | ENSP00000321874.5 | ||
B3GNT3 | ENST00000595387.1 | c.425G>A | p.Arg142His | missense_variant | Exon 2 of 3 | 1 | ENSP00000472638.1 | |||
B3GNT3 | ENST00000599265.5 | c.425G>A | p.Arg142His | missense_variant | Exon 2 of 3 | 3 | ENSP00000471733.1 | |||
B3GNT3 | ENST00000600777.1 | c.*43G>A | downstream_gene_variant | 3 | ENSP00000468914.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248696Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 135006
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461218Hom.: 0 Cov.: 36 AF XY: 0.00000275 AC XY: 2AN XY: 726866
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.425G>A (p.R142H) alteration is located in exon 2 (coding exon 1) of the B3GNT3 gene. This alteration results from a G to A substitution at nucleotide position 425, causing the arginine (R) at amino acid position 142 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at