1-115740722-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001232.4(CASQ2):c.420+6T>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 151,988 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001232.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CASQ2 | ENST00000261448.6 | c.420+6T>A | splice_region_variant, intron_variant | Intron 3 of 10 | 1 | NM_001232.4 | ENSP00000261448.5 | |||
CASQ2 | ENST00000488931.2 | n.144+6T>A | splice_region_variant, intron_variant | Intron 4 of 12 | 3 | ENSP00000518226.1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151988Hom.: 0 Cov.: 30
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 7.04e-7 AC: 1AN: 1420544Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 709362
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151988Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74226
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at