11-77039756-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138706.5(B3GNT6):c.205C>T(p.Pro69Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000527 in 1,594,462 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138706.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000269 AC: 41AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000626 AC: 13AN: 207760Hom.: 0 AF XY: 0.0000605 AC XY: 7AN XY: 115662
GnomAD4 exome AF: 0.0000298 AC: 43AN: 1442260Hom.: 0 Cov.: 30 AF XY: 0.0000293 AC XY: 21AN XY: 716648
GnomAD4 genome AF: 0.000269 AC: 41AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.205C>T (p.P69S) alteration is located in exon 2 (coding exon 1) of the B3GNT6 gene. This alteration results from a C to T substitution at nucleotide position 205, causing the proline (P) at amino acid position 69 to be replaced by a serine (S). 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