rs397514723
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PM5PP3
The NM_080605.4(B3GALT6):c.619G>A(p.Asp207Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000192 in 1,562,182 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D207E) has been classified as Uncertain significance.
Frequency
Consequence
NM_080605.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
B3GALT6 | NM_080605.4 | c.619G>A | p.Asp207Asn | missense_variant | 1/1 | ENST00000379198.5 | NP_542172.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
B3GALT6 | ENST00000379198.5 | c.619G>A | p.Asp207Asn | missense_variant | 1/1 | 6 | NM_080605.4 | ENSP00000368496.2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152072Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000142 AC: 2AN: 1410110Hom.: 0 Cov.: 31 AF XY: 0.00000286 AC XY: 2AN XY: 700376
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152072Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74288
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at