dbSNP rs17107764: KIF11:c.1702+9A>T (chr10-92632702-A-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004523.4(KIF11):c.1702+9A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0633 in 1,562,260 control chromosomes in the GnomAD database, including 8,146 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 3604 hom., cov: 32)

Exomes 𝑓: 0.054 ( 4542 hom. )

Consequence

KIF11
NM_004523.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.745

Publications

6 publications found

Variant links:

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

KIF11 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 10-92632702-A-T is Benign according to our data. Variant chr10-92632702-A-T is described in ClinVar as [Benign]. Clinvar id is 259408.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF11	NM_004523.4 link	c.1702+9A>T		intron_variant	Intron 13 of 21	ENST00000260731.5	NP_004514.2	P52732

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF11	ENST00000260731.5 link	c.1702+9A>T		intron_variant	Intron 13 of 21	1	NM_004523.4	ENSP00000260731.3		P52732

Frequencies

GnomAD3 genomes

AF:

0.149

AC:

22672

AN:

151916

Hom.:

3598

Cov.:

show subpopulations

Gnomad AFR

AF:

0.399

Gnomad AMI

AF:

0.136

Gnomad AMR

AF:

0.122

Gnomad ASJ

AF:

0.0493

Gnomad EAS

AF:

0.0949

Gnomad SAS

AF:

0.0786

Gnomad FIN

AF:

0.00775

Gnomad MID

AF:

0.115

Gnomad NFE

AF:

0.0409

Gnomad OTH

AF:

0.135

GnomAD2 exomes

AF:

0.0804

AC:

18194

AN:

226312

AF XY:

0.0736

show subpopulations

Gnomad AFR exome

AF:

0.410

Gnomad AMR exome

AF:

0.0972

Gnomad ASJ exome

AF:

0.0484

Gnomad EAS exome

AF:

0.115

Gnomad FIN exome

AF:

0.00886

Gnomad NFE exome

AF:

0.0411

Gnomad OTH exome

AF:

0.0631

GnomAD4 exome

AF:

0.0540

AC:

76140

AN:

1410226

Hom.:

4542

Cov.:

AF XY:

0.0533

AC XY:

37401

AN XY:

701202

show subpopulations

African (AFR)

AF:

0.413

AC:

13024

AN:

31502

American (AMR)

AF:

0.0946

AC:

3740

AN:

39554

Ashkenazi Jewish (ASJ)

AF:

0.0491

AC:

1193

AN:

24288

East Asian (EAS)

AF:

0.0895

AC:

3519

AN:

39308

South Asian (SAS)

AF:

0.0697

AC:

5632

AN:

80762

European-Finnish (FIN)

AF:

0.0111

AC:

582

AN:

52628

Middle Eastern (MID)

AF:

0.0926

AC:

513

AN:

5538

European-Non Finnish (NFE)

AF:

0.0407

AC:

43926

AN:

1078266

Other (OTH)

AF:

0.0687

AC:

4011

AN:

58380

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

3017

6034

9051

12068

15085

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1930

3860

5790

7720

9650

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.149

AC:

22713

AN:

152034

Hom.:

3604

Cov.:

AF XY:

0.144

AC XY:

10736

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.398

AC:

16510

AN:

41436

American (AMR)

AF:

0.122

AC:

1864

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.0493

AC:

171

AN:

3470

East Asian (EAS)

AF:

0.0950

AC:

489

AN:

5150

South Asian (SAS)

AF:

0.0774

AC:

373

AN:

4818

European-Finnish (FIN)

AF:

0.00775

AC:

AN:

10580

Middle Eastern (MID)

AF:

0.117

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.0409

AC:

2785

AN:

68024

Other (OTH)

AF:

0.134

AC:

281

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

775

1550

2324

3099

3874

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

206

412

618

824

1030

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0793

Hom.:

279

Bravo

AF:

0.166

Asia WGS

AF:

0.108

AC:

377

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

9.0

(source)

DANN

Benign

0.70

PhyloP100

0.74

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over