chr21-38299277-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_170736.3(KCNJ15):c.16A>G(p.Ile6Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 1,612,450 control chromosomes in the GnomAD database, including 141 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0077 ( 14 hom., cov: 33)
Exomes 𝑓: 0.011 ( 127 hom. )
Consequence
KCNJ15
NM_170736.3 missense
NM_170736.3 missense
Scores
16
Clinical Significance
Conservation
PhyloP100: -0.224
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0032828748).
BP6
?
Variant 21-38299277-A-G is Benign according to our data. Variant chr21-38299277-A-G is described in ClinVar as [Benign]. Clinvar id is 770817.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 14 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNJ15 | NM_170736.3 | c.16A>G | p.Ile6Val | missense_variant | 3/3 | ENST00000398938.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNJ15 | ENST00000398938.7 | c.16A>G | p.Ile6Val | missense_variant | 3/3 | 1 | NM_170736.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00765 AC: 1164AN: 152184Hom.: 14 Cov.: 33
GnomAD3 genomes
?
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1164
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152184
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33
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GnomAD3 exomes AF: 0.00854 AC: 2132AN: 249750Hom.: 21 AF XY: 0.00877 AC XY: 1184AN XY: 134982
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GnomAD4 exome AF: 0.0106 AC: 15522AN: 1460148Hom.: 127 Cov.: 31 AF XY: 0.0107 AC XY: 7736AN XY: 726144
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GnomAD4 genome ? AF: 0.00766 AC: 1166AN: 152302Hom.: 14 Cov.: 33 AF XY: 0.00691 AC XY: 515AN XY: 74480
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ESP6500EA
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108
ExAC
?
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1063
Asia WGS
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6
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3478
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 08, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.;.;.;.;.;.;T;T;.;T;T;T;T;T;T;.;T;T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;.;.;.;.;.;T;.;T;T;.;.;T;.;.;.;T;.;.;T;T
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N;N;N;N;.;.;N;N;N;N;N;N;N;N;N;N;N;N
REVEL
Benign
Sift4G
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T;.;T;T;T;T;T;T;T
Polyphen
0.0
.;.;.;.;.;.;.;B;B;.;.;B;.;.;B;B;.;B;B;.;.
Vest4
0.045, 0.069, 0.059, 0.055, 0.060
MVP
MPC
0.37
ClinPred
T
GERP RS
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gMVP
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