12-122207242-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_030765.4(B3GNT4):c.991C>T(p.Arg331Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,614,128 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030765.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
B3GNT4 | NM_030765.4 | c.991C>T | p.Arg331Trp | missense_variant | 3/3 | ENST00000324189.5 | |
B3GNT4 | NM_001330492.2 | c.916C>T | p.Arg306Trp | missense_variant | 2/2 | ||
B3GNT4 | XM_047429535.1 | c.916C>T | p.Arg306Trp | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
B3GNT4 | ENST00000324189.5 | c.991C>T | p.Arg331Trp | missense_variant | 3/3 | 1 | NM_030765.4 | A2 | |
B3GNT4 | ENST00000535274.1 | c.916C>T | p.Arg306Trp | missense_variant | 1/1 | P2 | |||
B3GNT4 | ENST00000546192.1 | c.916C>T | p.Arg306Trp | missense_variant | 2/2 | 2 | P2 | ||
B3GNT4 | ENST00000545141.1 | n.74-454C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152148Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251294Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135844
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461862Hom.: 0 Cov.: 34 AF XY: 0.00000825 AC XY: 6AN XY: 727236
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2023 | The c.991C>T (p.R331W) alteration is located in exon 3 (coding exon 2) of the B3GNT4 gene. This alteration results from a C to T substitution at nucleotide position 991, causing the arginine (R) at amino acid position 331 to be replaced by a tryptophan (W). 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