chr1-115740722-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001232.4(CASQ2):c.420+6T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 1,571,264 control chromosomes in the GnomAD database, including 558,295 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001232.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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CASQ2 | ENST00000261448.6 | c.420+6T>C | splice_region_variant, intron_variant | Intron 3 of 10 | 1 | NM_001232.4 | ENSP00000261448.5 | |||
CASQ2 | ENST00000488931.2 | n.144+6T>C | splice_region_variant, intron_variant | Intron 4 of 12 | 3 | ENSP00000518226.1 |
Frequencies
GnomAD3 genomes AF: 0.711 AC: 108052AN: 151940Hom.: 42127 Cov.: 30
GnomAD3 exomes AF: 0.796 AC: 199565AN: 250784Hom.: 81593 AF XY: 0.806 AC XY: 109246AN XY: 135562
GnomAD4 exome AF: 0.847 AC: 1202361AN: 1419206Hom.: 516157 Cov.: 24 AF XY: 0.846 AC XY: 599726AN XY: 708736
GnomAD4 genome AF: 0.711 AC: 108081AN: 152058Hom.: 42138 Cov.: 30 AF XY: 0.711 AC XY: 52849AN XY: 74322
ClinVar
Submissions by phenotype
Catecholaminergic polymorphic ventricular tachycardia 2 Benign:5
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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not specified Benign:3
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not provided Benign:2
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Catecholaminergic polymorphic ventricular tachycardia Benign:1
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Catecholaminergic polymorphic ventricular tachycardia 1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at