12-122206568-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_030765.4(B3GNT4):āc.317C>Gā(p.Ser106Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000681 in 1,614,122 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
B3GNT4 | NM_030765.4 | c.317C>G | p.Ser106Cys | missense_variant | Exon 3 of 3 | ENST00000324189.5 | NP_110392.1 | |
B3GNT4 | NM_001330492.2 | c.242C>G | p.Ser81Cys | missense_variant | Exon 2 of 2 | NP_001317421.1 | ||
B3GNT4 | XM_047429535.1 | c.242C>G | p.Ser81Cys | missense_variant | Exon 2 of 2 | XP_047285491.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152246Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251476Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135916
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461876Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727238
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.317C>G (p.S106C) alteration is located in exon 3 (coding exon 2) of the B3GNT4 gene. This alteration results from a C to G substitution at nucleotide position 317, causing the serine (S) at amino acid position 106 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