12-122206720-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_030765.4(B3GNT4):āc.469T>Cā(p.Phe157Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000137 in 1,609,282 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 (ā ).
Frequency
Consequence
NM_030765.4 missense
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
B3GNT4 | NM_030765.4 | c.469T>C | p.Phe157Leu | missense_variant | Exon 3 of 3 | ENST00000324189.5 | NP_110392.1 | |
B3GNT4 | NM_001330492.2 | c.394T>C | p.Phe132Leu | missense_variant | Exon 2 of 2 | NP_001317421.1 | ||
B3GNT4 | XM_047429535.1 | c.394T>C | p.Phe132Leu | missense_variant | Exon 2 of 2 | XP_047285491.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000122 AC: 3AN: 246380Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133394
GnomAD4 exome AF: 0.00000961 AC: 14AN: 1457196Hom.: 0 Cov.: 30 AF XY: 0.00000966 AC XY: 7AN XY: 724532
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152086Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.469T>C (p.F157L) alteration is located in exon 3 (coding exon 2) of the B3GNT4 gene. This alteration results from a T to C substitution at nucleotide position 469, causing the phenylalanine (F) at amino acid position 157 to be replaced by a leucine (L). 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