ENST00000676757.1:c.-131+13880G>A

Variant names:

• chr10-92588073-G-A
• rs6583826
• ENST00000676757.1:c.-131+13880G>A

Variant summary

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

The ENST00000676757.1(KIF11):​c.-131+13880G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 152,112 control chromosomes in the GnomAD database, including 22,244 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 0.54 (22244 hom., cov: 32)
• Consequence: KIF11 ENST00000676757.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 41 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=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF11	ENST00000676757.1	c.-131+13880G>A		intron_variant	Intron 1 of 21			ENSP00000504289.1

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81504 AN: 151994 Hom.: 22227 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.536 AC: 81570 AN: 152112 Hom.: 22244 Cov.: 32 AF XY: 0.537 AC XY: 39935 AN XY: 74336

African (AFR) AF: 0.510 AC: 21177 AN: 41514

American (AMR) AF: 0.504 AC: 7703 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2193 AN: 3472

East Asian (EAS) AF: 0.796 AC: 4111 AN: 5166

South Asian (SAS) AF: 0.692 AC: 3347 AN: 4834

European-Finnish (FIN) AF: 0.494 AC: 5218 AN: 10558

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 36029 AN: 67974

Other (OTH) AF: 0.542 AC: 1146 AN: 2116

Alfa AF: 0.539 Hom.: 71138

Bravo AF: 0.537

Asia WGS AF: 0.682 AC: 2373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	11
DANN	Benign	0.92
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs6583826; hg19: chr10-94347830;