10-92655321-A-C

Position:

• chr10-92655321-A-C

Variant summary

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

The NM_004523.4(KIF11):​c.*1525A>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 0.293 in 152,202 control chromosomes in the GnomAD database, including 7,866 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 0.29 (7866 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: KIF11 NM_004523.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.37

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=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF11	NM_004523.4	c.*1525A>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.*1525A>C		3_prime_UTR_variant	22/22	1	NM_004523.4	ENSP00000260731.3

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44596 AN: 152084 Hom.: 7870 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.310

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.293 AC: 44598 AN: 152202 Hom.: 7866 Cov.: 32 AF XY: 0.298 AC XY: 22176 AN XY: 74418

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.310

Alfa AF: 0.317 Hom.: 7238

Bravo AF: 0.278

Asia WGS AF: 0.502 AC: 1744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	9.6
DANN	Benign	0.68

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: rs1044153; hg19: chr10-94415078;