11-128839042-C-T
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_153766.3(KCNJ1):c.*83G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000238 in 1,262,682 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_153766.3 3_prime_UTR
Scores
Clinical Significance
Conservation
Publications
- Bartter disease type 2Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- antenatal Bartter syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCNJ1 | NM_153766.3 | c.*83G>A | 3_prime_UTR_variant | Exon 3 of 3 | ENST00000392666.6 | NP_722450.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152062Hom.: 0 Cov.: 32 show subpopulations
GnomAD4 exome AF: 0.0000180 AC: 20AN: 1110620Hom.: 0 Cov.: 15 AF XY: 0.0000194 AC XY: 11AN XY: 565822 show subpopulations
GnomAD4 genome AF: 0.0000658 AC: 10AN: 152062Hom.: 0 Cov.: 32 AF XY: 0.0000943 AC XY: 7AN XY: 74270 show subpopulations
ClinVar
Submissions by phenotype
Bartter disease type 2 Uncertain:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at