16-575837-A-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_ModeratePM2PP5_Moderate
The NM_004204.5(PIGQ):c.690-2A>G variant causes a splice acceptor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000709 in 1,409,580 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_004204.5 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 exomes AF: 0.00000571 AC: 1AN: 175014Hom.: 0 AF XY: 0.0000107 AC XY: 1AN XY: 93188
GnomAD4 exome AF: 7.09e-7 AC: 1AN: 1409580Hom.: 0 Cov.: 33 AF XY: 0.00000144 AC XY: 1AN XY: 696644
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 77 Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Apr 02, 2020 | This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PS3,PM2,PS4_SUPP. - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 15, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at