rs10736069

Variant names:

• chr10-92635636-T-C
• rs10736069
• NM_004523.4:c.1876-1548T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-92635636-T-C
• chr10-92635636-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004523.4(KIF11):​c.1876-1548T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,082 control chromosomes in the GnomAD database, including 38,545 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 (38545 hom., cov: 32)
• Consequence: KIF11 NM_004523.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 5 publications found

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]

KIF11 Gene-Disease associations (from GenCC):

• ciliopathy

  Inheritance: AD Classification: DEFINITIVE Submitted by: Ambry Genetics
• microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen, G2P

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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 rank	MANE	Protein	UniProt
KIF11	NM_004523.4	c.1876-1548T>C		intron_variant	Intron 14 of 21	ENST00000260731.5	NP_004514.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF11	ENST00000260731.5	c.1876-1548T>C		intron_variant	Intron 14 of 21	1	NM_004523.4	ENSP00000260731.3

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106244 AN: 151964 Hom.: 38490 Cov.: 32

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.699 AC: 106358 AN: 152082 Hom.: 38545 Cov.: 32 AF XY: 0.697 AC XY: 51850 AN XY: 74340

African (AFR) AF: 0.878 AC: 36399 AN: 41478

American (AMR) AF: 0.668 AC: 10207 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2319 AN: 3472

East Asian (EAS) AF: 0.926 AC: 4805 AN: 5188

South Asian (SAS) AF: 0.766 AC: 3692 AN: 4820

European-Finnish (FIN) AF: 0.584 AC: 6163 AN: 10554

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40498 AN: 67976

Other (OTH) AF: 0.667 AC: 1412 AN: 2116

Alfa AF: 0.651 Hom.: 4082

Bravo AF: 0.714

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	-0.89
CADD	Benign	5.5
DANN	Benign	0.60
PhyloP100		-0.63
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: rs10736069; hg19: chr10-94395393;