NM_016929.5:c.589-9_589-8delCT
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_016929.5(CLIC5):c.589-9_589-8delCT variant causes a splice region, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.372 in 1,573,906 control chromosomes in the GnomAD database, including 111,011 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_016929.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.338 AC: 51253AN: 151752Hom.: 8905 Cov.: 0
GnomAD3 exomes AF: 0.354 AC: 75576AN: 213610Hom.: 13882 AF XY: 0.363 AC XY: 41223AN XY: 113578
GnomAD4 exome AF: 0.376 AC: 534338AN: 1422036Hom.: 102102 AF XY: 0.377 AC XY: 264972AN XY: 702708
GnomAD4 genome AF: 0.338 AC: 51274AN: 151870Hom.: 8909 Cov.: 0 AF XY: 0.338 AC XY: 25083AN XY: 74188
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
c.1066-9_1066-8delCT in intron 5 of CLIC5: This variant is not expected to have clinical significance because it has been identified in 44.4% (8056/18162) of Ea st Asian chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.b roadinstitute.org/; dbSNP rs35735653). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at