chr5-96722706-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001750.7(CAST):c.270+8G>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 0.000142 in 1,603,102 control chromosomes in the GnomAD database, including 8 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 Likely benign (★).
Frequency
Consequence
NM_001750.7 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAST | NM_001750.7 | c.270+8G>A | splice_region_variant, intron_variant | ENST00000675179.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAST | ENST00000675179.1 | c.270+8G>A | splice_region_variant, intron_variant | NM_001750.7 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152248Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000302 AC: 76AN: 251374Hom.: 3 AF XY: 0.000456 AC XY: 62AN XY: 135856
GnomAD4 exome AF: 0.000148 AC: 215AN: 1450736Hom.: 8 Cov.: 27 AF XY: 0.000228 AC XY: 165AN XY: 722534
GnomAD4 genome ? AF: 0.0000853 AC: 13AN: 152366Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74512
ClinVar
Submissions by phenotype
CAST-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 28, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at