rs9968589

Variant names:

• chr5-170645374-G-A
• rs9968589
• NM_014592.4:c.62-73384G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-170645374-G-A
• chr5-170645374-G-T

Variant summary

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

The NM_014592.4(KCNIP1):​c.62-73384G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 151,950 control chromosomes in the GnomAD database, including 7,227 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 (7227 hom., cov: 32)
• Consequence: KCNIP1 NM_014592.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 1 publications found

Genes affected

KCNIP1 (HGNC:15521): (potassium voltage-gated channel interacting protein 1) This gene encodes a member of the family of cytosolic voltage-gated potassium (Kv) channel-interacting proteins (KCNIPs), which belong to the neuronal calcium sensor (NCS) family of the calcium binding EF-hand proteins. They associate with Kv4 alpha subunits to form native Kv4 channel complexes. The encoded protein may regulate rapidly inactivating (A-type) currents, and hence neuronal membrane excitability, in response to changes in the concentration of intracellular calcium. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2013]

KCNIP1-AS1 (HGNC:40710): (KCNIP1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014592.4. 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
	KCNIP1	NM_014592.4	MANE Select	c.62-73384G>A		intron	N/A	NP_055407.1	Q9NZI2-2
	KCNIP1	NM_001278339.2		c.62-73384G>A		intron	N/A	NP_001265268.1	Q9NZI2-5
	KCNIP1	NM_001034837.3		c.62-67480G>A		intron	N/A	NP_001030009.1	Q9NZI2-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNIP1	ENST00000328939.9	TSL:1 MANE Select	c.62-73384G>A		intron	N/A	ENSP00000329686.4	Q9NZI2-2
	KCNIP1	ENST00000434108.5	TSL:1	c.62-73384G>A		intron	N/A	ENSP00000414886.1	Q9NZI2-5
	KCNIP1	ENST00000411494.5	TSL:1	c.62-67480G>A		intron	N/A	ENSP00000395323.1	Q9NZI2-1

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42975 AN: 151830 Hom.: 7212 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.283 AC: 43025 AN: 151950 Hom.: 7227 Cov.: 32 AF XY: 0.281 AC XY: 20894 AN XY: 74290

African (AFR) AF: 0.473 AC: 19567 AN: 41398

American (AMR) AF: 0.174 AC: 2656 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 452 AN: 3468

East Asian (EAS) AF: 0.232 AC: 1203 AN: 5180

South Asian (SAS) AF: 0.225 AC: 1082 AN: 4810

European-Finnish (FIN) AF: 0.255 AC: 2684 AN: 10538

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14673 AN: 67954

Other (OTH) AF: 0.234 AC: 493 AN: 2108

Alfa AF: 0.228 Hom.: 13253

Bravo AF: 0.284

Asia WGS AF: 0.246 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.57
PhyloP100		0.33
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: rs9968589; hg19: chr5-170072378;