rs2068330

Variant summary

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

The NM_033272.4(KCNH7):​c.2963-859G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,842 control chromosomes in the GnomAD database, including 20,228 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 0.49 ( 20228 hom., cov: 31)

Consequence

KCNH7
NM_033272.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.335
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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KCNH7NM_033272.4 linkc.2963-859G>C intron_variant Intron 13 of 15 ENST00000332142.10 NP_150375.2 Q9NS40-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KCNH7ENST00000332142.10 linkc.2963-859G>C intron_variant Intron 13 of 15 1 NM_033272.4 ENSP00000331727.5 Q9NS40-1

Frequencies

GnomAD3 genomes
AF:
0.490
AC:
74316
AN:
151724
Hom.:
20178
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.702
Gnomad AMI
AF:
0.392
Gnomad AMR
AF:
0.469
Gnomad ASJ
AF:
0.494
Gnomad EAS
AF:
0.825
Gnomad SAS
AF:
0.452
Gnomad FIN
AF:
0.403
Gnomad MID
AF:
0.472
Gnomad NFE
AF:
0.358
Gnomad OTH
AF:
0.458
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.490
AC:
74423
AN:
151842
Hom.:
20228
Cov.:
31
AF XY:
0.495
AC XY:
36688
AN XY:
74184
show subpopulations
Gnomad4 AFR
AF:
0.703
Gnomad4 AMR
AF:
0.470
Gnomad4 ASJ
AF:
0.494
Gnomad4 EAS
AF:
0.825
Gnomad4 SAS
AF:
0.451
Gnomad4 FIN
AF:
0.403
Gnomad4 NFE
AF:
0.358
Gnomad4 OTH
AF:
0.461
Alfa
AF:
0.426
Hom.:
1893
Bravo
AF:
0.507
Asia WGS
AF:
0.620
AC:
2151
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.42
DANN
Benign
0.62

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: rs2068330; hg19: chr2-163237390; API