6-39191171-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_003740.4(KCNK5):​c.1219G>A​(p.Ala407Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00335 in 1,614,206 control chromosomes in the GnomAD database, including 16 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 (★).

Frequency

Genomes: 𝑓 0.0033 ( 1 hom., cov: 31)
Exomes 𝑓: 0.0034 ( 15 hom. )

Consequence

KCNK5
NM_003740.4 missense

Scores

1
17

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.46
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 -10 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0027202666).
BP6
Variant 6-39191171-C-T is Benign according to our data. Variant chr6-39191171-C-T is described in ClinVar as [Benign]. Clinvar id is 790348.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAdExome4 at 15 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KCNK5NM_003740.4 linkuse as main transcriptc.1219G>A p.Ala407Thr missense_variant 5/5 ENST00000359534.4
KCNK5XM_005249456.2 linkuse as main transcriptc.1210G>A p.Ala404Thr missense_variant 5/5
KCNK5XM_006715235.2 linkuse as main transcriptc.673G>A p.Ala225Thr missense_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KCNK5ENST00000359534.4 linkuse as main transcriptc.1219G>A p.Ala407Thr missense_variant 5/51 NM_003740.4 P1

Frequencies

GnomAD3 genomes
AF:
0.00328
AC:
500
AN:
152212
Hom.:
1
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000555
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00105
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00207
Gnomad FIN
AF:
0.0183
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00375
Gnomad OTH
AF:
0.000955
GnomAD3 exomes
AF:
0.00377
AC:
948
AN:
251414
Hom.:
6
AF XY:
0.00390
AC XY:
530
AN XY:
135900
show subpopulations
Gnomad AFR exome
AF:
0.000800
Gnomad AMR exome
AF:
0.000694
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00157
Gnomad FIN exome
AF:
0.0187
Gnomad NFE exome
AF:
0.00380
Gnomad OTH exome
AF:
0.00407
GnomAD4 exome
AF:
0.00336
AC:
4908
AN:
1461876
Hom.:
15
Cov.:
32
AF XY:
0.00328
AC XY:
2383
AN XY:
727242
show subpopulations
Gnomad4 AFR exome
AF:
0.000358
Gnomad4 AMR exome
AF:
0.000760
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00146
Gnomad4 FIN exome
AF:
0.0175
Gnomad4 NFE exome
AF:
0.00327
Gnomad4 OTH exome
AF:
0.00260
GnomAD4 genome
AF:
0.00328
AC:
500
AN:
152330
Hom.:
1
Cov.:
31
AF XY:
0.00399
AC XY:
297
AN XY:
74478
show subpopulations
Gnomad4 AFR
AF:
0.000553
Gnomad4 AMR
AF:
0.00105
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00207
Gnomad4 FIN
AF:
0.0183
Gnomad4 NFE
AF:
0.00375
Gnomad4 OTH
AF:
0.000945
Alfa
AF:
0.00327
Hom.:
2
Bravo
AF:
0.00208
TwinsUK
AF:
0.00270
AC:
10
ALSPAC
AF:
0.00363
AC:
14
ESP6500AA
AF:
0.000454
AC:
2
ESP6500EA
AF:
0.00349
AC:
30
ExAC
AF:
0.00362
AC:
440
Asia WGS
AF:
0.000866
AC:
3
AN:
3478
EpiCase
AF:
0.00409
EpiControl
AF:
0.00338

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 testingLabcorp Genetics (formerly Invitae), LabcorpNov 02, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.066
BayesDel_addAF
Benign
-0.59
T
BayesDel_noAF
Benign
-0.62
CADD
Benign
17
DANN
Uncertain
0.98
DEOGEN2
Benign
0.13
T
Eigen
Benign
-0.70
Eigen_PC
Benign
-0.60
FATHMM_MKL
Benign
0.70
D
LIST_S2
Benign
0.70
T
MetaRNN
Benign
0.0027
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.4
L
MutationTaster
Benign
0.86
N
PrimateAI
Benign
0.28
T
PROVEAN
Benign
-0.57
N
REVEL
Benign
0.062
Sift
Benign
0.067
T
Sift4G
Benign
0.54
T
Polyphen
0.0040
B
Vest4
0.021
MVP
0.19
MPC
0.65
ClinPred
0.013
T
GERP RS
2.2
Varity_R
0.037
gMVP
0.17

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs147451811; hg19: chr6-39158947; COSMIC: COSV63988862; API