rs2240116
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_032634.4(PIGO):c.512-17C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0598 in 1,594,534 control chromosomes in the GnomAD database, including 5,463 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_032634.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0672 AC: 10224AN: 152152Hom.: 600 Cov.: 32
GnomAD3 exomes AF: 0.0898 AC: 20753AN: 231066Hom.: 1655 AF XY: 0.0876 AC XY: 11002AN XY: 125662
GnomAD4 exome AF: 0.0591 AC: 85191AN: 1442264Hom.: 4862 Cov.: 32 AF XY: 0.0612 AC XY: 43908AN XY: 717684
GnomAD4 genome AF: 0.0672 AC: 10227AN: 152270Hom.: 601 Cov.: 32 AF XY: 0.0715 AC XY: 5322AN XY: 74448
ClinVar
Submissions by phenotype
not specified Benign:2
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Hyperphosphatasia with intellectual disability syndrome 2 Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at