rs7078243

Positions:

• chr10-92654506-A-C
• chr10-92654506-A-T

Variant summary

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

The ENST00000260731.5(KIF11):​c.*710A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,904 control chromosomes in the GnomAD database, including 28,800 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 0.60 (28800 hom., cov: 31)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: KIF11 ENST00000260731.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

KIF11 (HGNC:6388): (kinesin family member 11) This gene encodes a motor protein that belongs to the kinesin-like protein family. Members of this protein family are known to be involved in various kinds of spindle dynamics. The function of this gene product includes chromosome positioning, centrosome separation and establishing a bipolar spindle during cell mitosis. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF11	NM_004523.4	c.*710A>C		3_prime_UTR_variant	22/22	ENST00000260731.5	NP_004514.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF11	ENST00000260731.5	c.*710A>C		3_prime_UTR_variant	22/22	1	NM_004523.4	ENSP00000260731	P1

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91568 AN: 151778 Hom.: 28762 Cov.: 31

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.582

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.603 AC: 91649 AN: 151898 Hom.: 28800 Cov.: 31 AF XY: 0.600 AC XY: 44533 AN XY: 74228

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.580

Alfa AF: 0.528 Hom.: 40495

Bravo AF: 0.611

Asia WGS AF: 0.672 AC: 2334 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.48
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		0.97

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs7078243; hg19: chr10-94414263;