rs16870787

Variant names:

• chr4-21314989-T-C
• rs16870787
• NM_025221.6:c.62-432280A>G

Variant summary

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

The NM_025221.6(KCNIP4):​c.62-432280A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0368 in 152,310 control chromosomes in the GnomAD database, including 209 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 0.037 (209 hom., cov: 32)
• Consequence: KCNIP4 NM_025221.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.935
• Publications: 1 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]

ENSG00000250243 (HGNC:41254):

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 (SAS) allele frequency at 95% confidence interval = 0.12 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.62-432280A>G		intron	N/A	NP_079497.2
	KCNIP4	NM_001035003.2		c.88+382361A>G		intron	N/A	NP_001030175.1	Q6PIL6-5
	KCNIP4	NM_147181.4		c.62-464322A>G		intron	N/A	NP_671710.1	Q6PIL6-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNIP4	ENST00000382152.7	TSL:5 MANE Select	c.62-432280A>G		intron	N/A	ENSP00000371587.2	Q6PIL6-1
	KCNIP4	ENST00000382148.7	TSL:1	c.88+382361A>G		intron	N/A	ENSP00000371583.3	Q6PIL6-5
	KCNIP4	ENST00000509207.1	TSL:1	c.-24+229401A>G		intron	N/A	ENSP00000423257.1	Q6PIL6-3

Frequencies

GnomAD3 genomes AF: 0.0367 AC: 5587 AN: 152192 Hom.: 208 Cov.: 32

Gnomad AFR AF: 0.0393

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.0556

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0291

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0154

Gnomad OTH AF: 0.0253

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

GnomAD4 genome AF: 0.0368 AC: 5608 AN: 152310 Hom.: 209 Cov.: 32 AF XY: 0.0393 AC XY: 2926 AN XY: 74488

African (AFR) AF: 0.0394 AC: 1636 AN: 41562

American (AMR) AF: 0.102 AC: 1566 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0144 AC: 50 AN: 3472

East Asian (EAS) AF: 0.0561 AC: 291 AN: 5184

South Asian (SAS) AF: 0.128 AC: 617 AN: 4824

European-Finnish (FIN) AF: 0.0291 AC: 309 AN: 10630

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0154 AC: 1050 AN: 68024

Other (OTH) AF: 0.0269 AC: 57 AN: 2116

Alfa AF: 0.0242 Hom.: 509

Bravo AF: 0.0413

Asia WGS AF: 0.109 AC: 379 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	0.13
DANN	Benign	0.77
PhyloP100		-0.94
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs16870787; hg19: chr4-21316612;