13-91448869-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004466.6(GPC5):c.272C>T(p.Thr91Met) variant causes a missense change. The variant allele was found at a frequency of 0.000268 in 1,613,636 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004466.6 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: 0.000381 AC: 58AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000355 AC: 89AN: 250974Hom.: 0 AF XY: 0.000280 AC XY: 38AN XY: 135626
GnomAD4 exome AF: 0.000256 AC: 374AN: 1461400Hom.: 1 Cov.: 30 AF XY: 0.000246 AC XY: 179AN XY: 726996
GnomAD4 genome AF: 0.000381 AC: 58AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.000417 AC XY: 31AN XY: 74420
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.272C>T (p.T91M) alteration is located in exon 2 (coding exon 2) of the GPC5 gene. This alteration results from a C to T substitution at nucleotide position 272, causing the threonine (T) at amino acid position 91 to be replaced by a methionine (M). 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