17-63910419-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_022579.3(CSHL1):c.306+1G>A variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000507 in 1,614,218 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_022579.3 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00247 AC: 376AN: 152214Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000799 AC: 201AN: 251484Hom.: 1 AF XY: 0.000640 AC XY: 87AN XY: 135910
GnomAD4 exome AF: 0.000303 AC: 443AN: 1461886Hom.: 3 Cov.: 84 AF XY: 0.000268 AC XY: 195AN XY: 727244
GnomAD4 genome AF: 0.00247 AC: 376AN: 152332Hom.: 2 Cov.: 32 AF XY: 0.00217 AC XY: 162AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:1
CSHL1: BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at