rs527236156
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_001194958.2(KCNJ18):c.1195C>T(p.Arg399Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00175 in 1,601,800 control chromosomes in the GnomAD database, including 58 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0092 ( 25 hom., cov: 35)
Exomes 𝑓: 0.00097 ( 33 hom. )
Consequence
KCNJ18
NM_001194958.2 stop_gained
NM_001194958.2 stop_gained
Scores
2
4
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.70
Genes affected
KCNJ18 (HGNC:39080): (potassium inwardly rectifying channel subfamily J member 18) This gene encodes a member of the inwardly rectifying potassium channel family. Transcription of this locus is regulated by thyroid hormone, and the encoded protein plays a role in resting membrane potential maintenance. Mutations in this locus have been associated with thyrotoxic hypokalemic periodic paralysis. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00916 (1395/152302) while in subpopulation AFR AF= 0.0321 (1334/41556). AF 95% confidence interval is 0.0307. There are 25 homozygotes in gnomad4. There are 626 alleles in male gnomad4 subpopulation. Median coverage is 35. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1395 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNJ18 | NM_001194958.2 | c.1195C>T | p.Arg399Ter | stop_gained | 3/3 | ENST00000567955.3 | |
KCNJ18 | XM_005276919.4 | c.1501C>T | p.Arg501Ter | stop_gained | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNJ18 | ENST00000567955.3 | c.1195C>T | p.Arg399Ter | stop_gained | 3/3 | 1 | NM_001194958.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00912 AC: 1388AN: 152184Hom.: 25 Cov.: 35
GnomAD3 genomes
?
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35
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GnomAD4 exome AF: 0.000971 AC: 1408AN: 1449498Hom.: 33 Cov.: 35 AF XY: 0.000859 AC XY: 619AN XY: 720188
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GnomAD4 genome ? AF: 0.00916 AC: 1395AN: 152302Hom.: 25 Cov.: 35 AF XY: 0.00841 AC XY: 626AN XY: 74458
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?
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ESP6500AA
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66
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ExAC
?
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277
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MutationTaster
Benign
D;D
Vest4
GERP RS
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at