rs7675300

Positions:

• chr4-21383914-C-A
• chr4-21383914-C-G
• chr4-21383914-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_025221.6(KCNIP4):​c.62-501205G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,016 control chromosomes in the GnomAD database, including 6,632 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 (6632 hom., cov: 31)
• Consequence: KCNIP4 NM_025221.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410

Genes affected

KCNIP4 (HGNC:30083): (potassium voltage-gated channel interacting protein 4) This gene encodes a member of the family of voltage-gated potassium (Kv) channel-interacting proteins (KCNIPs), which belong to the recoverin branch of the EF-hand superfamily. Members of the KCNIP family are small calcium binding proteins. They all have EF-hand-like domains, and differ from each other in the N-terminus. They are integral subunit components of native Kv4 channel complexes. They may regulate A-type currents, and hence neuronal excitability, in response to changes in intracellular calcium. This protein member also interacts with presenilin. Multiple alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

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 = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNIP4	NM_025221.6	c.62-501205G>T		intron_variant		ENST00000382152.7	NP_079497.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNIP4	ENST00000382152.7	c.62-501205G>T		intron_variant		5	NM_025221.6	ENSP00000371587

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41822 AN: 151898 Hom.: 6627 Cov.: 31

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.275 AC: 41840 AN: 152016 Hom.: 6632 Cov.: 31 AF XY: 0.281 AC XY: 20883 AN XY: 74290

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.258

Alfa AF: 0.280 Hom.: 1130

Bravo AF: 0.251

Asia WGS AF: 0.370 AC: 1285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.34

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7675300; hg19: chr4-21385537;