rs16869942

Variant names:

• chr4-20766079-C-G
• rs16869942
• NM_025221.6:c.289-7189G>C

Your query was ambiguous. Multiple possible variants found:

• chr4-20766079-C-G
• chr4-20766079-C-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.289-7189G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0285 in 152,172 control chromosomes in the GnomAD database, including 106 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 0.029 (106 hom., cov: 32)
• Consequence: KCNIP4 NM_025221.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.236
• 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]

PACRGL (HGNC:28442): (parkin coregulated like)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNIP4	NM_025221.6	c.289-7189G>C		intron_variant	Intron 3 of 8	ENST00000382152.7	NP_079497.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCNIP4	ENST00000382152.7	c.289-7189G>C		intron_variant	Intron 3 of 8	5	NM_025221.6	ENSP00000371587.2

Frequencies

GnomAD3 genomes AF: 0.0286 AC: 4345 AN: 152054 Hom.: 104 Cov.: 32

Gnomad AFR AF: 0.00539

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0800

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.0889

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.0332

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0270

Gnomad OTH AF: 0.0368

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

GnomAD4 genome AF: 0.0285 AC: 4344 AN: 152172 Hom.: 106 Cov.: 32 AF XY: 0.0297 AC XY: 2209 AN XY: 74386

African (AFR) AF: 0.00537 AC: 223 AN: 41526

American (AMR) AF: 0.0801 AC: 1224 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0242 AC: 84 AN: 3472

East Asian (EAS) AF: 0.0895 AC: 463 AN: 5172

South Asian (SAS) AF: 0.0112 AC: 54 AN: 4810

European-Finnish (FIN) AF: 0.0332 AC: 352 AN: 10590

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0270 AC: 1834 AN: 68002

Other (OTH) AF: 0.0354 AC: 75 AN: 2116

Alfa AF: 0.0279 Hom.: 14

Bravo AF: 0.0323

Asia WGS AF: 0.0470 AC: 163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.36
PhyloP100		0.24
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: rs16869942; hg19: chr4-20767702;