rs1064273
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_170736.3(KCNJ15):c.*988C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 166,932 control chromosomes in the GnomAD database, including 19,816 homozygotes. 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
Genomes: 𝑓 0.46 ( 17927 hom., cov: 33)
Exomes 𝑓: 0.50 ( 1889 hom. )
Consequence
KCNJ15
NM_170736.3 3_prime_UTR
NM_170736.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.133
Genes affected
KCNJ15 (HGNC:6261): (potassium inwardly rectifying channel subfamily J member 15) Potassium channels are present in most mammalian cells, where they participate in a wide range of physiologic responses. The protein encoded by this gene is an integral membrane protein and inward-rectifier type potassium channel. The encoded protein has a greater tendency to allow potassium to flow into a cell rather than out of a cell. Eight transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Feb 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNJ15 | NM_170736.3 | c.*988C>T | 3_prime_UTR_variant | 3/3 | ENST00000398938.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNJ15 | ENST00000398938.7 | c.*988C>T | 3_prime_UTR_variant | 3/3 | 1 | NM_170736.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.463 AC: 70275AN: 151930Hom.: 17931 Cov.: 33
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GnomAD4 exome AF: 0.504 AC: 7507AN: 14884Hom.: 1889 Cov.: 0 AF XY: 0.505 AC XY: 3569AN XY: 7070
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GnomAD4 genome ? AF: 0.462 AC: 70286AN: 152048Hom.: 17927 Cov.: 33 AF XY: 0.458 AC XY: 34025AN XY: 74310
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at