Genetic Variant KIF3A:c.1130-40C>G (chr5-132711097-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001300791.2(KIF3A):c.1130-40C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 1,576,946 control chromosomes in the GnomAD database, including 389,390 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 0.59 ( 28553 hom., cov: 30)

Exomes 𝑓: 0.70 ( 360837 hom. )

Consequence

KIF3A
NM_001300791.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.304

Publications

17 publications found

Variant links:

Genes affected

KIF3A (HGNC:6319): (kinesin family member 3A) Enables protein phosphatase binding activity; small GTPase binding activity; and spectrin binding activity. Involved in protein localization to cell junction and protein transport. Located in centriole and centrosome. Part of kinesin II complex. Colocalizes with spindle microtubule. [provided by Alliance of Genome Resources, Apr 2022]

KIF3A links:

ENSG00000230612 (HGNC:):

ENSG00000230612 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF3A	NM_001300791.2 link	c.1130-40C>G		intron_variant	Intron 8 of 18	ENST00000403231.6	NP_001287720.1	Q9Y496E9PES4B4DHG8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF3A	ENST00000403231.6 link	c.1130-40C>G		intron_variant	Intron 8 of 18	2	NM_001300791.2	ENSP00000385808.1		E9PES4

Frequencies

GnomAD3 genomes

AF:

0.590

AC:

89521

AN:

151708

Hom.:

28553

Cov.:

show subpopulations

Gnomad AFR

AF:

0.400

Gnomad AMI

AF:

0.908

Gnomad AMR

AF:

0.562

Gnomad ASJ

AF:

0.714

Gnomad EAS

AF:

0.166

Gnomad SAS

AF:

0.647

Gnomad FIN

AF:

0.537

Gnomad MID

AF:

0.684

Gnomad NFE

AF:

0.735

Gnomad OTH

AF:

0.637

GnomAD2 exomes

AF:

0.601

AC:

150116

AN:

249878

AF XY:

0.620

show subpopulations

Gnomad AFR exome

AF:

0.392

Gnomad AMR exome

AF:

0.412

Gnomad ASJ exome

AF:

0.725

Gnomad EAS exome

AF:

0.141

Gnomad FIN exome

AF:

0.545

Gnomad NFE exome

AF:

0.740

Gnomad OTH exome

AF:

0.662

GnomAD4 exome

AF:

0.699

AC:

996747

AN:

1425122

Hom.:

360837

Cov.:

AF XY:

0.701

AC XY:

498444

AN XY:

711106

show subpopulations

African (AFR)

AF:

0.394

AC:

12946

AN:

32840

American (AMR)

AF:

0.429

AC:

18990

AN:

44282

Ashkenazi Jewish (ASJ)

AF:

0.722

AC:

18677

AN:

25872

East Asian (EAS)

AF:

0.183

AC:

7247

AN:

39502

South Asian (SAS)

AF:

0.666

AC:

56829

AN:

85296

European-Finnish (FIN)

AF:

0.552

AC:

29444

AN:

53350

Middle Eastern (MID)

AF:

0.689

AC:

3933

AN:

5708

European-Non Finnish (NFE)

AF:

0.750

AC:

808986

AN:

1079106

Other (OTH)

AF:

0.671

AC:

39695

AN:

59166

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

11377

22754

34132

45509

56886

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19130

38260

57390

76520

95650

<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:

0.590

AC:

89548

AN:

151824

Hom.:

28553

Cov.:

AF XY:

0.579

AC XY:

42950

AN XY:

74192

show subpopulations

African (AFR)

AF:

0.400

AC:

16527

AN:

41334

American (AMR)

AF:

0.562

AC:

8578

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.714

AC:

2476

AN:

3470

East Asian (EAS)

AF:

0.167

AC:

859

AN:

5158

South Asian (SAS)

AF:

0.648

AC:

3120

AN:

4812

European-Finnish (FIN)

AF:

0.537

AC:

5650

AN:

10512

Middle Eastern (MID)

AF:

0.680

AC:

200

AN:

294

European-Non Finnish (NFE)

AF:

0.735

AC:

49974

AN:

67960

Other (OTH)

AF:

0.634

AC:

1336

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1635

3270

4904

6539

8174

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

736

1472

2208

2944

3680

<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:

0.663

Hom.:

6170

Bravo

AF:

0.577

Asia WGS

AF:

0.449

AC:

1563

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

9.3

(source)

DANN

Benign

0.49

PhyloP100

0.30

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

Computational scores

Splicing

Publications

Other links and lift over