GeneBe

chr14-63006481-GAA-G

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_139318.5(KCNH5):​c.198-11_198-10delTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000761 in 1,314,684 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 7.6e-7 ( 0 hom. )

Consequence

KCNH5
NM_139318.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.114

Publications

0 publications found
Variant links:
Genes affected
KCNH5 (HGNC:6254): (potassium voltage-gated channel subfamily H member 5) This gene encodes a member of voltage-gated potassium channels. Members of this family have diverse functions, including regulating neurotransmitter and hormone release, cardiac function, and cell volume. This protein is an outward-rectifying, noninactivating channel. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
KCNH5 Gene-Disease associations (from GenCC):
  • infantile-onset epilepsy
    Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
  • developmental and epileptic encephalopathy 112
    Inheritance: AD Classification: STRONG Submitted by: G2P

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_139318.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
KCNH5
NM_139318.5
MANE Select
c.198-11_198-10delTT
intron
N/ANP_647479.2
KCNH5
NM_172375.3
c.198-11_198-10delTT
intron
N/ANP_758963.1Q8NCM2-2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
KCNH5
ENST00000322893.12
TSL:1 MANE Select
c.198-11_198-10delTT
intron
N/AENSP00000321427.7Q8NCM2-1
KCNH5
ENST00000420622.6
TSL:1
c.198-11_198-10delTT
intron
N/AENSP00000395439.2Q8NCM2-2
KCNH5
ENST00000394964.3
TSL:1
n.363-11_363-10delTT
intron
N/A

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
7.61e-7
AC:
1
AN:
1314684
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
659852
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
30042
American (AMR)
AF:
0.00
AC:
0
AN:
41696
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24732
East Asian (EAS)
AF:
0.00
AC:
0
AN:
38692
South Asian (SAS)
AF:
0.00
AC:
0
AN:
79994
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
51816
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5426
European-Non Finnish (NFE)
AF:
0.00000101
AC:
1
AN:
987110
Other (OTH)
AF:
0.00
AC:
0
AN:
55176
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.11

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

Other links and lift over

dbSNP: rs36103415; hg19: chr14-63473199; COSMIC: COSV100526815; API