4-21204867-T-A

Variant names:

• chr4-21204867-T-A
• rs1023721
• NM_025221.6:c.62-322158A>T

Variant summary

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

The NM_025221.6(KCNIP4):​c.62-322158A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0652 in 152,242 control chromosomes in the GnomAD database, including 390 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 0.065 (390 hom., cov: 33)
• Consequence: KCNIP4 NM_025221.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 4 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025221.6. 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
	KCNIP4	NM_025221.6	MANE Select	c.62-322158A>T		intron	N/A	NP_079497.2
	KCNIP4	NM_147183.3		c.100+98940A>T		intron	N/A	NP_671712.1	Q6PIL6-4
	KCNIP4	NM_001035003.2		c.89-354200A>T		intron	N/A	NP_001030175.1	Q6PIL6-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNIP4	ENST00000382152.7	TSL:5 MANE Select	c.62-322158A>T		intron	N/A	ENSP00000371587.2	Q6PIL6-1
	KCNIP4	ENST00000382150.8	TSL:1	c.100+98940A>T		intron	N/A	ENSP00000371585.4	Q6PIL6-4
	KCNIP4	ENST00000382148.7	TSL:1	c.89-354200A>T		intron	N/A	ENSP00000371583.3	Q6PIL6-5

Frequencies

GnomAD3 genomes AF: 0.0652 AC: 9913 AN: 152124 Hom.: 386 Cov.: 33

Gnomad AFR AF: 0.0445

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0436

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.0485

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0664

Gnomad OTH AF: 0.0750

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

GnomAD4 genome AF: 0.0652 AC: 9930 AN: 152242 Hom.: 390 Cov.: 33 AF XY: 0.0650 AC XY: 4841 AN XY: 74442

African (AFR) AF: 0.0447 AC: 1857 AN: 41548

American (AMR) AF: 0.116 AC: 1769 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0436 AC: 151 AN: 3466

East Asian (EAS) AF: 0.149 AC: 772 AN: 5170

South Asian (SAS) AF: 0.0292 AC: 141 AN: 4826

European-Finnish (FIN) AF: 0.0485 AC: 515 AN: 10612

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0664 AC: 4519 AN: 68016

Other (OTH) AF: 0.0733 AC: 155 AN: 2114

Alfa AF: 0.0623 Hom.: 44

Bravo AF: 0.0710

Asia WGS AF: 0.0720 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.051
DANN	Benign	0.61
PhyloP100		-1.9
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: rs1023721; hg19: chr4-21206490;