NM_016929.5:c.588+1480T>C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_016929.5(CLIC5):c.588+1480T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00859 in 1,518,520 control chromosomes in the GnomAD database, including 417 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_016929.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0194 AC: 2954AN: 152146Hom.: 81 Cov.: 33
GnomAD3 exomes AF: 0.0233 AC: 3211AN: 137778Hom.: 100 AF XY: 0.0215 AC XY: 1602AN XY: 74604
GnomAD4 exome AF: 0.00737 AC: 10076AN: 1366256Hom.: 336 Cov.: 25 AF XY: 0.00762 AC XY: 5147AN XY: 675404
GnomAD4 genome AF: 0.0195 AC: 2962AN: 152264Hom.: 81 Cov.: 33 AF XY: 0.0213 AC XY: 1585AN XY: 74452
ClinVar
Submissions by phenotype
not specified Benign:1
c.589-9T>C in intron 5 of CLIC5: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue, is not located with in the splice consensus sequence, and has been identified in 5.73% (11/192) of E ast Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.bro adinstitute.org; dbSNP rs75878754). -
CLIC5-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at