rs12732939

Variant names:

• chr1-44755760-C-T
• rs12732939
• NM_006845.4:c.760-169C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
KIF2C	NM_006845.4	c.760-169C>T		intron_variant	Intron 8 of 20	ENST00000372224.9	NP_006836.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF2C	ENST00000372224.9	c.760-169C>T		intron_variant	Intron 8 of 20	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

African (AFR) AF: 0.457 AC: 18960 AN: 41458

American (AMR) AF: 0.221 AC: 3372 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 567 AN: 3470

East Asian (EAS) AF: 0.276 AC: 1427 AN: 5170

South Asian (SAS) AF: 0.186 AC: 896 AN: 4826

European-Finnish (FIN) AF: 0.179 AC: 1896 AN: 10594

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11842 AN: 67996

Other (OTH) AF: 0.228 AC: 481 AN: 2110

Alfa AF: 0.244 Hom.: 718

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
PhyloP100		-0.76
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: rs12732939; hg19: chr1-45221432;