12-122206811-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_030765.4(B3GNT4):c.560C>A(p.Thr187Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000627 in 1,611,968 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/14 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
B3GNT4 | NM_030765.4 | c.560C>A | p.Thr187Asn | missense_variant | 3/3 | ENST00000324189.5 | NP_110392.1 | |
B3GNT4 | NM_001330492.2 | c.485C>A | p.Thr162Asn | missense_variant | 2/2 | NP_001317421.1 | ||
B3GNT4 | XM_047429535.1 | c.485C>A | p.Thr162Asn | missense_variant | 2/2 | XP_047285491.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
B3GNT4 | ENST00000324189.5 | c.560C>A | p.Thr187Asn | missense_variant | 3/3 | 1 | NM_030765.4 | ENSP00000319636 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249212Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134770
GnomAD4 exome AF: 0.0000685 AC: 100AN: 1459786Hom.: 0 Cov.: 30 AF XY: 0.0000675 AC XY: 49AN XY: 726126
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 14, 2024 | The c.560C>A (p.T187N) alteration is located in exon 3 (coding exon 2) of the B3GNT4 gene. This alteration results from a C to A substitution at nucleotide position 560, causing the threonine (T) at amino acid position 187 to be replaced by an asparagine (N). 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