rs12732939

Positions:

• chr1-44755760-C-T

Variant summary

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

The NM_006845.4(KIF2C):​c.760-169C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,104 control chromosomes in the GnomAD database, including 6,485 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 0.26 (6485 hom., cov: 32)
• Consequence: KIF2C NM_006845.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757

Genes affected

KIF2C (HGNC:6393): (kinesin family member 2C) This gene encodes a kinesin-like protein that functions as a microtubule-dependent molecular motor. The encoded protein can depolymerize microtubules at the plus end, thereby promoting mitotic chromosome segregation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

KIF2C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF2C	NM_006845.4	c.760-169C>T		intron_variant		ENST00000372224.9	NP_006836.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF2C	ENST00000372224.9	c.760-169C>T		intron_variant		1	NM_006845.4	ENSP00000361298.4

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39541 AN: 151986 Hom.: 6482 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.260 AC: 39573 AN: 152104 Hom.: 6485 Cov.: 32 AF XY: 0.257 AC XY: 19113 AN XY: 74362

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.228

Alfa AF: 0.236 Hom.: 630

Bravo AF: 0.271

Asia WGS AF: 0.239 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.32
DANN	Benign	0.17

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

Publications

LitVar

Other links and lift over

dbSNP: rs12732939; hg19: chr1-45221432;