2-98533401-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001134225.2(INPP4A):c.176C>T(p.Ser59Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000155 in 1,613,104 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001134225.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000683 AC: 17AN: 248928Hom.: 0 AF XY: 0.0000889 AC XY: 12AN XY: 135022
GnomAD4 exome AF: 0.000164 AC: 239AN: 1460786Hom.: 1 Cov.: 29 AF XY: 0.000167 AC XY: 121AN XY: 726674
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152318Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.176C>T (p.S59L) alteration is located in exon 5 (coding exon 3) of the INPP4A gene. This alteration results from a C to T substitution at nucleotide position 176, causing the serine (S) at amino acid position 59 to be replaced by a leucine (L). 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