1-230988440-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_022786.3(ARV1):c.294+1G>A variant causes a splice donor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000059 in 1,526,642 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_022786.3 splice_donor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARV1 | NM_022786.3 | c.294+1G>A | splice_donor_variant | ENST00000310256.7 | NP_073623.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARV1 | ENST00000310256.7 | c.294+1G>A | splice_donor_variant | 1 | NM_022786.3 | ENSP00000312458 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000953 AC: 2AN: 209808Hom.: 0 AF XY: 0.00000876 AC XY: 1AN XY: 114150
GnomAD4 exome AF: 0.00000582 AC: 8AN: 1374516Hom.: 0 Cov.: 28 AF XY: 0.00000587 AC XY: 4AN XY: 681960
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74316
ClinVar
Submissions by phenotype
ARV1-related disorder Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Department of Women and Children's Health, University of New South Wales | Feb 13, 2015 | Segregates with epileptic encephalopathy in family. Clinical phenotype consistent with previous patient reported with ARV1 related disorder. - |
Developmental and epileptic encephalopathy, 38 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 23, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at