2-162551742-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_033272.4(KCNH7):​c.308-14662T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,046 control chromosomes in the GnomAD database, including 9,500 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.31 ( 9500 hom., cov: 32)

Consequence

KCNH7
NM_033272.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.773
Variant links:
Genes affected
KCNH7 (HGNC:18863): (potassium voltage-gated channel subfamily H member 7) Voltage-gated potassium (Kv) channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoints. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. This gene encodes a member of the potassium channel, voltage-gated, subfamily H. This member is a pore-forming (alpha) subunit. There are at least two alternatively spliced transcript variants derived from this gene and encoding distinct isoforms. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KCNH7NM_033272.4 linkuse as main transcriptc.308-14662T>C intron_variant ENST00000332142.10 NP_150375.2 Q9NS40-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KCNH7ENST00000332142.10 linkuse as main transcriptc.308-14662T>C intron_variant 1 NM_033272.4 ENSP00000331727.5 Q9NS40-1
KCNH7ENST00000328032.8 linkuse as main transcriptc.308-14662T>C intron_variant 1 ENSP00000333781.4 Q9NS40-2

Frequencies

GnomAD3 genomes
AF:
0.308
AC:
46828
AN:
151928
Hom.:
9509
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0825
Gnomad AMI
AF:
0.454
Gnomad AMR
AF:
0.286
Gnomad ASJ
AF:
0.371
Gnomad EAS
AF:
0.00733
Gnomad SAS
AF:
0.198
Gnomad FIN
AF:
0.378
Gnomad MID
AF:
0.347
Gnomad NFE
AF:
0.464
Gnomad OTH
AF:
0.341
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.308
AC:
46807
AN:
152046
Hom.:
9500
Cov.:
32
AF XY:
0.299
AC XY:
22205
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.0823
Gnomad4 AMR
AF:
0.286
Gnomad4 ASJ
AF:
0.371
Gnomad4 EAS
AF:
0.00734
Gnomad4 SAS
AF:
0.198
Gnomad4 FIN
AF:
0.378
Gnomad4 NFE
AF:
0.464
Gnomad4 OTH
AF:
0.337
Alfa
AF:
0.378
Hom.:
2482
Bravo
AF:
0.290
Asia WGS
AF:
0.107
AC:
373
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
7.1
DANN
Benign
0.86

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: rs12185647; hg19: chr2-163408252; API