6-39190997-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_003740.4(KCNK5):​c.1393C>A​(p.Pro465Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00313 in 1,576,484 control chromosomes in the GnomAD database, including 139 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.017 ( 70 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 69 hom. )

Consequence

KCNK5
NM_003740.4 missense

Scores

3
15

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.76
Variant links:
Genes affected
KCNK5 (HGNC:6280): (potassium two pore domain channel subfamily K member 5) This gene encodes one of the members of the superfamily of potassium channel proteins containing two pore-forming P domains. The message for this gene is mainly expressed in the cortical distal tubules and collecting ducts of the kidney. The protein is highly sensitive to external pH and this, in combination with its expression pattern, suggests it may play an important role in renal potassium transport. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0019867122).
BP6
Variant 6-39190997-G-T is Benign according to our data. Variant chr6-39190997-G-T is described in ClinVar as [Benign]. Clinvar id is 1239991.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0568 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KCNK5NM_003740.4 linkuse as main transcriptc.1393C>A p.Pro465Thr missense_variant 5/5 ENST00000359534.4
KCNK5XM_005249456.2 linkuse as main transcriptc.1384C>A p.Pro462Thr missense_variant 5/5
KCNK5XM_006715235.2 linkuse as main transcriptc.847C>A p.Pro283Thr missense_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KCNK5ENST00000359534.4 linkuse as main transcriptc.1393C>A p.Pro465Thr missense_variant 5/51 NM_003740.4 P1

Frequencies

GnomAD3 genomes
AF:
0.0170
AC:
2584
AN:
152198
Hom.:
70
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0589
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00654
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000206
Gnomad OTH
AF:
0.0120
GnomAD3 exomes
AF:
0.00437
AC:
900
AN:
206138
Hom.:
18
AF XY:
0.00281
AC XY:
312
AN XY:
111080
show subpopulations
Gnomad AFR exome
AF:
0.0576
Gnomad AMR exome
AF:
0.00295
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000252
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000107
Gnomad OTH exome
AF:
0.000802
GnomAD4 exome
AF:
0.00165
AC:
2345
AN:
1424168
Hom.:
69
Cov.:
32
AF XY:
0.00142
AC XY:
1005
AN XY:
705432
show subpopulations
Gnomad4 AFR exome
AF:
0.0615
Gnomad4 AMR exome
AF:
0.00336
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000125
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000411
Gnomad4 OTH exome
AF:
0.00309
GnomAD4 genome
AF:
0.0170
AC:
2583
AN:
152316
Hom.:
70
Cov.:
32
AF XY:
0.0162
AC XY:
1210
AN XY:
74486
show subpopulations
Gnomad4 AFR
AF:
0.0587
Gnomad4 AMR
AF:
0.00653
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000206
Gnomad4 OTH
AF:
0.0118
Alfa
AF:
0.00401
Hom.:
19
Bravo
AF:
0.0191
ESP6500AA
AF:
0.0552
AC:
243
ESP6500EA
AF:
0.000233
AC:
2
ExAC
AF:
0.00507
AC:
615
Asia WGS
AF:
0.00231
AC:
9
AN:
3476

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 submitterclinical testingGeneDxOct 29, 2020This variant is associated with the following publications: (PMID: 26220970) -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.070
BayesDel_addAF
Benign
-0.56
T
BayesDel_noAF
Benign
-0.54
CADD
Benign
21
DANN
Benign
0.97
DEOGEN2
Benign
0.17
T
Eigen
Uncertain
0.21
Eigen_PC
Uncertain
0.33
FATHMM_MKL
Uncertain
0.89
D
LIST_S2
Benign
0.73
T
MetaRNN
Benign
0.0020
T
MetaSVM
Benign
-1.2
T
MutationAssessor
Benign
1.3
L
MutationTaster
Benign
0.51
N
PrimateAI
Benign
0.48
T
PROVEAN
Benign
-1.3
N
REVEL
Benign
0.16
Sift
Benign
0.12
T
Sift4G
Benign
0.29
T
Polyphen
0.78
P
Vest4
0.31
MVP
0.20
MPC
0.77
ClinPred
0.019
T
GERP RS
5.9
Varity_R
0.064
gMVP
0.22

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9462487; hg19: chr6-39158773; API