1-16024780-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004070.4(CLCNKA):c.247A>G(p.Arg83Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 1,613,634 control chromosomes in the GnomAD database, including 257,855 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004070.4 missense
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 rank | MANE | Protein | UniProt |
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CLCNKA | NM_004070.4 | c.247A>G | p.Arg83Gly | missense_variant | Exon 4 of 20 | ENST00000331433.5 | NP_004061.3 | |
CLCNKA | NM_001042704.2 | c.247A>G | p.Arg83Gly | missense_variant | Exon 4 of 20 | NP_001036169.1 | ||
CLCNKA | NM_001257139.2 | c.229+852A>G | intron_variant | Intron 3 of 18 | NP_001244068.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.592 AC: 89861AN: 151908Hom.: 27307 Cov.: 32
GnomAD3 exomes AF: 0.551 AC: 138274AN: 251076Hom.: 39379 AF XY: 0.553 AC XY: 75081AN XY: 135786
GnomAD4 exome AF: 0.559 AC: 816601AN: 1461608Hom.: 230521 Cov.: 60 AF XY: 0.559 AC XY: 406144AN XY: 727106
GnomAD4 genome AF: 0.592 AC: 89927AN: 152026Hom.: 27334 Cov.: 32 AF XY: 0.584 AC XY: 43408AN XY: 74290
ClinVar
Submissions by phenotype
not provided Benign:3
This variant is associated with the following publications: (PMID: 23850580, 21248228) -
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Bartter disease type 4B Benign:2
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not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at