rs3765023

Variant names:

• chr2-162771755-G-A
• rs3765023
• NM_033272.4:c.307+64782C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033272.4(KCNH7):​c.307+64782C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 151,560 control chromosomes in the GnomAD database, including 6,991 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 0.28 (6991 hom., cov: 32)
• Consequence: KCNH7 NM_033272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 3 publications found

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]

KCNH7-AS1 (HGNC:40858): (KCNH7 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033272.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNH7	NM_033272.4	MANE Select	c.307+64782C>T		intron	N/A	NP_150375.2
	KCNH7	NM_173162.3		c.307+64782C>T		intron	N/A	NP_775185.1	Q9NS40-2
	KCNH7-AS1	NR_110258.2		n.54-176G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNH7	ENST00000332142.10	TSL:1 MANE Select	c.307+64782C>T		intron	N/A	ENSP00000331727.5	Q9NS40-1
	KCNH7	ENST00000328032.8	TSL:1	c.307+64782C>T		intron	N/A	ENSP00000333781.4	Q9NS40-2
	KCNH7-AS1	ENST00000446838.2	TSL:1	n.54-176G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42682 AN: 151444 Hom.: 6971 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.276

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.282 AC: 42736 AN: 151560 Hom.: 6991 Cov.: 32 AF XY: 0.282 AC XY: 20873 AN XY: 74020

African (AFR) AF: 0.460 AC: 18995 AN: 41338

American (AMR) AF: 0.279 AC: 4248 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 911 AN: 3468

East Asian (EAS) AF: 0.306 AC: 1574 AN: 5142

South Asian (SAS) AF: 0.146 AC: 703 AN: 4814

European-Finnish (FIN) AF: 0.227 AC: 2371 AN: 10442

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.194 AC: 13159 AN: 67822

Other (OTH) AF: 0.275 AC: 577 AN: 2102

Alfa AF: 0.228 Hom.: 930

Bravo AF: 0.299

Asia WGS AF: 0.244 AC: 851 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.29
PhyloP100		-0.16
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3765023; hg19: chr2-163628265;