dbSNP rs2299006: KIF3A:c.1229-68G>C (chr5-132709046-C-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001300791.2(KIF3A):c.1229-68G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 1,206,280 control chromosomes in the GnomAD database, including 39,854 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 0.32 ( 10971 hom., cov: 32)

Exomes 𝑓: 0.19 ( 28883 hom. )

Consequence

KIF3A
NM_001300791.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.420

Publications

5 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 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.1229-68G>C	intron	N/A	NP_001287720.1
KIF3A	NM_001300792.2		c.1228+1913G>C	intron	N/A	NP_001287721.1
KIF3A	NM_007054.7		c.1228+1913G>C	intron	N/A	NP_008985.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
KIF3A	ENST00000403231.6	TSL:2 MANE Select	c.1229-68G>C	intron	N/A	ENSP00000385808.1
KIF3A	ENST00000378735.5	TSL:1	c.1228+1913G>C	intron	N/A	ENSP00000368009.1
KIF3A	ENST00000618515.4	TSL:5	c.1230-72G>C	intron	N/A	ENSP00000483023.1

Frequencies

GnomAD3 genomes

AF:

0.321

AC:

48769

AN:

151840

Hom.:

10941

Cov.:

show subpopulations

Gnomad AFR

AF:

0.579

Gnomad AMI

AF:

0.0165

Gnomad AMR

AF:

0.324

Gnomad ASJ

AF:

0.151

Gnomad EAS

AF:

0.755

Gnomad SAS

AF:

0.184

Gnomad FIN

AF:

0.358

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.150

Gnomad OTH

AF:

0.257

GnomAD4 exome

AF:

0.187

AC:

197640

AN:

1054322

Hom.:

28883

AF XY:

0.184

AC XY:

98114

AN XY:

533398

show subpopulations

African (AFR)

AF:

0.585

AC:

14073

AN:

24048

American (AMR)

AF:

0.423

AC:

13717

AN:

32414

Ashkenazi Jewish (ASJ)

AF:

0.149

AC:

3346

AN:

22404

East Asian (EAS)

AF:

0.718

AC:

24406

AN:

34012

South Asian (SAS)

AF:

0.157

AC:

11003

AN:

69870

European-Finnish (FIN)

AF:

0.343

AC:

15550

AN:

45292

Middle Eastern (MID)

AF:

0.136

AC:

680

AN:

5018

European-Non Finnish (NFE)

AF:

0.135

AC:

104819

AN:

774780

Other (OTH)

AF:

0.216

AC:

10046

AN:

46484

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

6742

13484

20227

26969

33711

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3514

7028

10542

14056

17570

<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:

0.322

AC:

48857

AN:

151958

Hom.:

10971

Cov.:

AF XY:

0.331

AC XY:

24553

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.580

AC:

23989

AN:

41382

American (AMR)

AF:

0.324

AC:

4955

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.151

AC:

523

AN:

3470

East Asian (EAS)

AF:

0.754

AC:

3903

AN:

5176

South Asian (SAS)

AF:

0.183

AC:

879

AN:

4816

European-Finnish (FIN)

AF:

0.358

AC:

3778

AN:

10558

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.150

AC:

10224

AN:

67972

Other (OTH)

AF:

0.260

AC:

548

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1413

2827

4240

5654

7067

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

442

884

1326

1768

2210

<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:

0.138

Hom.:

293

Bravo

AF:

0.337

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

(source)

DANN

Benign

0.72

PhyloP100

-0.42

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