chr10-92654810-A-T

Position:

• chr10-92654810-A-T

Variant summary

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

The NM_004523.4(KIF11):​c.*1014A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,496 control chromosomes in the GnomAD database, including 38,731 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 0.70 (38657 hom., cov: 32)
  • Exomes 𝑓: 0.63 (74 hom.)
• Consequence: KIF11 NM_004523.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF11	NM_004523.4	c.*1014A>T		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.*1014A>T		3_prime_UTR_variant	22/22	1	NM_004523.4	ENSP00000260731.3

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106377 AN: 152000 Hom.: 38602 Cov.: 32

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.668

GnomAD4 exome AF: 0.635 AC: 240 AN: 378 Hom.: 74 Cov.: 0 AF XY: 0.640 AC XY: 137 AN XY: 214

Gnomad4 FIN exome AF: 0.633

Gnomad4 NFE exome AF: 0.667

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.700 AC: 106491 AN: 152118 Hom.: 38657 Cov.: 32 AF XY: 0.698 AC XY: 51908 AN XY: 74354

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.926

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.668

Alfa AF: 0.535 Hom.: 1585

Bravo AF: 0.715

Asia WGS AF: 0.806 AC: 2803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.85
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs4933734; hg19: chr10-94414567;