rs35351345
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_000085.5(CLCNKB):c.1297+5G>T variant causes a splice region, intron change. The variant allele was found at a frequency of 0.00705 in 1,614,038 control chromosomes in the GnomAD database, including 47 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000085.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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CLCNKB | NM_000085.5 | c.1297+5G>T | splice_region_variant, intron_variant | Intron 13 of 19 | ENST00000375679.9 | NP_000076.2 | ||
CLCNKB | NM_001165945.2 | c.790+5G>T | splice_region_variant, intron_variant | Intron 6 of 12 | NP_001159417.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00523 AC: 796AN: 152118Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00570 AC: 1434AN: 251492Hom.: 6 AF XY: 0.00566 AC XY: 769AN XY: 135920
GnomAD4 exome AF: 0.00724 AC: 10587AN: 1461802Hom.: 45 Cov.: 34 AF XY: 0.00716 AC XY: 5205AN XY: 727206
GnomAD4 genome AF: 0.00522 AC: 795AN: 152236Hom.: 2 Cov.: 32 AF XY: 0.00478 AC XY: 356AN XY: 74438
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:3
CLCNKB: PP3, BS2 -
BS1, BS2, PP3 -
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Intronic +5 splice site variant in a gene for which loss-of-function is a known mechanism of disease, and splice predictors support a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge -
not specified Uncertain:1Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at