dbSNP rs72811230: KIF11:c.2770+16A>G (chr10-92648450-A-G) – 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.2770+16A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0678 in 1,492,596 control chromosomes in the GnomAD database, including 4,040 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.053 ( 288 hom., cov: 32)

Exomes 𝑓: 0.070 ( 3752 hom. )

Consequence

KIF11
NM_004523.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 2.29

Publications

5 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: ClinGen, G2P, Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics

KIF11 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_004523.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.55).

BP6

Variant 10-92648450-A-G is Benign according to our data. Variant chr10-92648450-A-G is described in ClinVar as Benign. ClinVar VariationId is 259410.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0718 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004523.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF11	NM_004523.4	MANE Select	c.2770+16A>G		intron	N/A	NP_004514.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
KIF11	ENST00000260731.5	TSL:1 MANE Select	c.2770+16A>G	intron	N/A	ENSP00000260731.3	P52732
KIF11	ENST00000937278.1		c.2605+181A>G	intron	N/A	ENSP00000607337.1
KIF11	ENST00000676647.1		c.2563+16A>G	intron	N/A	ENSP00000503394.1	A0A7I2V3A9

Frequencies

GnomAD3 genomes

AF:

0.0526

AC:

8007

AN:

152190

Hom.:

288

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0151

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.0492

Gnomad ASJ

AF:

0.0952

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0155

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0735

Gnomad OTH

AF:

0.0546

GnomAD2 exomes

AF:

0.0582

AC:

11805

AN:

202986

AF XY:

0.0587

show subpopulations

Gnomad AFR exome

AF:

0.0125

Gnomad AMR exome

AF:

0.0385

Gnomad ASJ exome

AF:

0.101

Gnomad EAS exome

AF:

0.000129

Gnomad FIN exome

AF:

0.0985

Gnomad NFE exome

AF:

0.0742

Gnomad OTH exome

AF:

0.0696

GnomAD4 exome

AF:

0.0696

AC:

93218

AN:

1340286

Hom.:

3752

Cov.:

AF XY:

0.0682

AC XY:

45576

AN XY:

668118

show subpopulations

African (AFR)

AF:

0.0124

AC:

356

AN:

28772

American (AMR)

AF:

0.0406

AC:

1314

AN:

32396

Ashkenazi Jewish (ASJ)

AF:

0.101

AC:

2343

AN:

23220

East Asian (EAS)

AF:

0.0000795

AC:

AN:

37714

South Asian (SAS)

AF:

0.0195

AC:

1473

AN:

75478

European-Finnish (FIN)

AF:

0.0936

AC:

4864

AN:

51970

Middle Eastern (MID)

AF:

0.0592

AC:

304

AN:

5136

European-Non Finnish (NFE)

AF:

0.0767

AC:

79034

AN:

1029868

Other (OTH)

AF:

0.0633

AC:

3527

AN:

55732

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

4069

8137

12206

16274

20343

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2844

5688

8532

11376

14220

<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:

0.0525

AC:

8003

AN:

152310

Hom.:

288

Cov.:

AF XY:

0.0533

AC XY:

3969

AN XY:

74474

show subpopulations

African (AFR)

AF:

0.0151

AC:

626

AN:

41582

American (AMR)

AF:

0.0492

AC:

752

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0952

AC:

330

AN:

3468

East Asian (EAS)

AF:

0.000578

AC:

AN:

5190

South Asian (SAS)

AF:

0.0157

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.101

AC:

1069

AN:

10602

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0735

AC:

4997

AN:

68022

Other (OTH)

AF:

0.0540

AC:

114

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

391

782

1173

1564

1955

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

264

352

440

<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:

0.0508

Hom.:

Bravo

AF:

0.0482

Asia WGS

AF:

0.00837

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

not specified (3)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

(source)

DANN

Benign

0.87

PhyloP100

2.3

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over