10-69157082-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_004896.5(VPS26A):c.305C>T(p.Thr102Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000093 in 1,613,634 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 (★).
Frequency
Consequence
NM_004896.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251154Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135756
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461358Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 726976
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.305C>T (p.T102I) alteration is located in exon 4 (coding exon 4) of the VPS26A gene. This alteration results from a C to T substitution at nucleotide position 305, causing the threonine (T) at amino acid position 102 to be replaced by an isoleucine (I). 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