Genetic Variant KIF3A:c.1938+87A>G (chr5-132700560-T-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.1938+87A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.873 in 873,044 control chromosomes in the GnomAD database, including 333,713 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 0.86 ( 55878 hom., cov: 30)

Exomes 𝑓: 0.88 ( 277835 hom. )

Consequence

KIF3A
NM_001300791.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.957

Publications

12 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001300791.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
KIF3A	NM_001300791.2	MANE Select	c.1938+87A>G	intron	N/A	NP_001287720.1
KIF3A	NM_001300792.2		c.1866+87A>G	intron	N/A	NP_001287721.1
KIF3A	NM_007054.7		c.1857+87A>G	intron	N/A	NP_008985.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
KIF3A	ENST00000403231.6	TSL:2 MANE Select	c.1938+87A>G	intron	N/A	ENSP00000385808.1
KIF3A	ENST00000378735.5	TSL:1	c.1866+87A>G	intron	N/A	ENSP00000368009.1
KIF3A	ENST00000487055.1	TSL:3	n.707A>G	non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.855

AC:

130071

AN:

152054

Hom.:

55862

Cov.:

show subpopulations

Gnomad AFR

AF:

0.789

Gnomad AMI

AF:

0.925

Gnomad AMR

AF:

0.862

Gnomad ASJ

AF:

0.864

Gnomad EAS

AF:

0.920

Gnomad SAS

AF:

0.829

Gnomad FIN

AF:

0.893

Gnomad MID

AF:

0.801

Gnomad NFE

AF:

0.885

Gnomad OTH

AF:

0.854

GnomAD4 exome

AF:

0.877

AC:

632271

AN:

720872

Hom.:

277835

Cov.:

AF XY:

0.875

AC XY:

335951

AN XY:

384156

show subpopulations

African (AFR)

AF:

0.792

AC:

14341

AN:

18100

American (AMR)

AF:

0.844

AC:

28900

AN:

34228

Ashkenazi Jewish (ASJ)

AF:

0.869

AC:

16934

AN:

19492

East Asian (EAS)

AF:

0.908

AC:

32944

AN:

36274

South Asian (SAS)

AF:

0.821

AC:

53044

AN:

64648

European-Finnish (FIN)

AF:

0.892

AC:

46073

AN:

51636

Middle Eastern (MID)

AF:

0.815

AC:

3430

AN:

4208

European-Non Finnish (NFE)

AF:

0.888

AC:

405619

AN:

456784

Other (OTH)

AF:

0.873

AC:

30986

AN:

35502

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

3917

7834

11752

15669

19586

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4568

9136

13704

18272

22840

<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:

0.855

AC:

130133

AN:

152172

Hom.:

55878

Cov.:

AF XY:

0.854

AC XY:

63507

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.788

AC:

32686

AN:

41486

American (AMR)

AF:

0.862

AC:

13180

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.864

AC:

2999

AN:

3472

East Asian (EAS)

AF:

0.920

AC:

4766

AN:

5182

South Asian (SAS)

AF:

0.829

AC:

3987

AN:

4810

European-Finnish (FIN)

AF:

0.893

AC:

9457

AN:

10594

Middle Eastern (MID)

AF:

0.806

AC:

237

AN:

294

European-Non Finnish (NFE)

AF:

0.885

AC:

60173

AN:

68016

Other (OTH)

AF:

0.854

AC:

1806

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

951

1902

2853

3804

4755

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

894

1788

2682

3576

4470

<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:

0.872

Hom.:

110063

Bravo

AF:

0.849

Asia WGS

AF:

0.890

AC:

3097

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.5

(source)

DANN

Benign

0.80

PhyloP100

-0.96

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over