12-122206769-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_030765.4(B3GNT4):āc.518A>Gā(p.Tyr173Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000317 in 1,606,792 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_030765.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
B3GNT4 | NM_030765.4 | c.518A>G | p.Tyr173Cys | missense_variant | Exon 3 of 3 | ENST00000324189.5 | NP_110392.1 | |
B3GNT4 | NM_001330492.2 | c.443A>G | p.Tyr148Cys | missense_variant | Exon 2 of 2 | NP_001317421.1 | ||
B3GNT4 | XM_047429535.1 | c.443A>G | p.Tyr148Cys | missense_variant | Exon 2 of 2 | XP_047285491.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000326 AC: 8AN: 245416Hom.: 0 AF XY: 0.0000377 AC XY: 5AN XY: 132732
GnomAD4 exome AF: 0.0000296 AC: 43AN: 1454654Hom.: 0 Cov.: 30 AF XY: 0.0000346 AC XY: 25AN XY: 722940
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.518A>G (p.Y173C) alteration is located in exon 3 (coding exon 2) of the B3GNT4 gene. This alteration results from a A to G substitution at nucleotide position 518, causing the tyrosine (Y) at amino acid position 173 to be replaced by a cysteine (C). 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