6-39191171-C-T
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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
NM_003740.4 missense
Scores
1
17
Clinical Significance
Conservation
PhyloP100: 2.46
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]
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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=0.0027202666).
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 |
---|---|---|---|---|---|---|---|
KCNK5 | NM_003740.4 | c.1219G>A | p.Ala407Thr | missense_variant | 5/5 | ENST00000359534.4 | |
KCNK5 | XM_005249456.2 | c.1210G>A | p.Ala404Thr | missense_variant | 5/5 | ||
KCNK5 | XM_006715235.2 | c.673G>A | p.Ala225Thr | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNK5 | ENST00000359534.4 | c.1219G>A | p.Ala407Thr | missense_variant | 5/5 | 1 | NM_003740.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00328 AC: 500AN: 152212Hom.: 1 Cov.: 31
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GnomAD3 exomes AF: 0.00377 AC: 948AN: 251414Hom.: 6 AF XY: 0.00390 AC XY: 530AN XY: 135900
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GnomAD4 exome AF: 0.00336 AC: 4908AN: 1461876Hom.: 15 Cov.: 32 AF XY: 0.00328 AC XY: 2383AN XY: 727242
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GnomAD4 genome AF: 0.00328 AC: 500AN: 152330Hom.: 1 Cov.: 31 AF XY: 0.00399 AC XY: 297AN XY: 74478
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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 | Nov 02, 2017 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
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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