1-16032437-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004070.4(CLCNKA):c.1846-6T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 1,608,830 control chromosomes in the GnomAD database, including 372,657 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 Benign (★★).
Frequency
Consequence
NM_004070.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLCNKA | NM_004070.4 | c.1846-6T>C | splice_region_variant, intron_variant | ENST00000331433.5 | NP_004061.3 | |||
CLCNKA | NM_001042704.2 | c.1846-9T>C | intron_variant | NP_001036169.1 | ||||
CLCNKA | NM_001257139.2 | c.1717-6T>C | splice_region_variant, intron_variant | NP_001244068.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLCNKA | ENST00000331433.5 | c.1846-6T>C | splice_region_variant, intron_variant | 1 | NM_004070.4 | ENSP00000332771.4 | ||||
CLCNKA | ENST00000375692.5 | c.1846-9T>C | intron_variant | 1 | ENSP00000364844.1 | |||||
CLCNKA | ENST00000439316.6 | c.1717-6T>C | splice_region_variant, intron_variant | 2 | ENSP00000414445.2 | |||||
CLCNKA | ENST00000464764.5 | n.2450-6T>C | splice_region_variant, intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.701 AC: 106598AN: 152028Hom.: 37803 Cov.: 33
GnomAD3 exomes AF: 0.682 AC: 171024AN: 250740Hom.: 59411 AF XY: 0.678 AC XY: 91983AN XY: 135700
GnomAD4 exome AF: 0.675 AC: 983127AN: 1456684Hom.: 334827 Cov.: 35 AF XY: 0.673 AC XY: 487813AN XY: 724878
GnomAD4 genome AF: 0.701 AC: 106675AN: 152146Hom.: 37830 Cov.: 33 AF XY: 0.699 AC XY: 52020AN XY: 74384
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 09, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 06, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Bartter disease type 4B Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 22, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at