10-92592861-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000676647.1(KIF11):c.-131+1032C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,208 control chromosomes in the GnomAD database, including 3,367 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.13 (3367 hom., cov: 33)
• Consequence: KIF11 ENST00000676647.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.217

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 10-92592861-C-T is Benign according to our data. Variant chr10-92592861-C-T is described in ClinVar as [Benign]. Clinvar id is 1287156.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF11	ENST00000676647.1	c.-131+1032C>T		intron_variant
KIF11	ENST00000676757.1	c.-130-13404C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19523 AN: 152090 Hom.: 3361 Cov.: 33

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0697

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.0648

Gnomad FIN AF: 0.00198

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0178

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.128 AC: 19557 AN: 152208 Hom.: 3367 Cov.: 33 AF XY: 0.124 AC XY: 9222 AN XY: 74434

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.0694

Gnomad4 ASJ AF: 0.0352

Gnomad4 EAS AF: 0.0528

Gnomad4 SAS AF: 0.0636

Gnomad4 FIN AF: 0.00198

Gnomad4 NFE AF: 0.0178

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0585 Hom.: 244

Bravo AF: 0.144

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 08, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	5.8
Dann	Benign	0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11187084; hg19: chr10-94352618;