2-162813784-C-T

Variant summary

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

The NM_033272.4(KCNH7):​c.307+22753G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.941 in 152,250 control chromosomes in the GnomAD database, including 67,486 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 0.94 ( 67486 hom., cov: 32)

Consequence

KCNH7
NM_033272.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.430
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=-0.9).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KCNH7NM_033272.4 linkuse as main transcriptc.307+22753G>A intron_variant ENST00000332142.10 NP_150375.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KCNH7ENST00000332142.10 linkuse as main transcriptc.307+22753G>A intron_variant 1 NM_033272.4 ENSP00000331727 P1Q9NS40-1
KCNH7ENST00000328032.8 linkuse as main transcriptc.307+22753G>A intron_variant 1 ENSP00000333781 Q9NS40-2

Frequencies

GnomAD3 genomes
AF:
0.941
AC:
143114
AN:
152130
Hom.:
67436
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.881
Gnomad AMI
AF:
0.954
Gnomad AMR
AF:
0.967
Gnomad ASJ
AF:
0.995
Gnomad EAS
AF:
0.914
Gnomad SAS
AF:
0.966
Gnomad FIN
AF:
0.968
Gnomad MID
AF:
0.994
Gnomad NFE
AF:
0.963
Gnomad OTH
AF:
0.963
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.941
AC:
143224
AN:
152250
Hom.:
67486
Cov.:
32
AF XY:
0.942
AC XY:
70116
AN XY:
74418
show subpopulations
Gnomad4 AFR
AF:
0.881
Gnomad4 AMR
AF:
0.967
Gnomad4 ASJ
AF:
0.995
Gnomad4 EAS
AF:
0.914
Gnomad4 SAS
AF:
0.967
Gnomad4 FIN
AF:
0.968
Gnomad4 NFE
AF:
0.963
Gnomad4 OTH
AF:
0.963
Alfa
AF:
0.943
Hom.:
9135
Bravo
AF:
0.937
Asia WGS
AF:
0.937
AC:
3258
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
4.3
DANN
Benign
0.22

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: rs3843856; hg19: chr2-163670294; COSMIC: COSV59811293; API