dbSNP rs41289846: KIF3B:c.*3009G>A (chr20-32334328-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_004798.4(KIF3B):c.*3009G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0305 in 152,666 control chromosomes in the GnomAD database, including 115 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 0.030 ( 112 hom., cov: 32)

Exomes 𝑓: 0.076 ( 3 hom. )

Consequence

KIF3B
NM_004798.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.39

Publications

2 publications found

Variant links:

Genes affected

KIF3B (HGNC:6320): (kinesin family member 3B) The protein encoded by this gene acts as a heterodimer with kinesin family member 3A to aid in chromosome movement during mitosis and meiosis. The encoded protein is a plus end-directed microtubule motor and can interact with the SMC3 subunit of the cohesin complex. In addition, the encoded protein may be involved in the intracellular movement of membranous organelles. This protein and kinesin family member 3A form the kinesin II subfamily of the kinesin superfamily. [provided by RefSeq, Jul 2008]

KIF3B Gene-Disease associations (from GenCC):

retinitis pigmentosa 89
Inheritance: AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
ciliopathy
Inheritance: AD Classification: MODERATE, LIMITED Submitted by: Franklin by Genoox, G2P

KIF3B links:

Genome browser will be placed here

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=-0.85).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0304 (4623/152150) while in subpopulation NFE AF = 0.045 (3063/68016). AF 95% confidence interval is 0.0437. There are 112 homozygotes in GnomAd4. There are 2309 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High AC in GnomAd4 at 4623 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
KIF3B	NM_004798.4 link	c.*3009G>A	3_prime_UTR_variant	Exon 9 of 9	ENST00000375712.4	NP_004789.1	O15066-1
KIF3B	XM_047440589.1 link	c.*3009G>A	3_prime_UTR_variant	Exon 9 of 9		XP_047296545.1
KIF3B	XM_047440590.1 link	c.*3009G>A	3_prime_UTR_variant	Exon 9 of 9		XP_047296546.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF3B	ENST00000375712.4 link	c.*3009G>A		3_prime_UTR_variant	Exon 9 of 9	1	NM_004798.4	ENSP00000364864.3		O15066-1

Frequencies

GnomAD3 genomes

AF:

0.0304

AC:

4627

AN:

152032

Hom.:

113

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00727

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.0183

Gnomad ASJ

AF:

0.0150

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.00663

Gnomad FIN

AF:

0.0803

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0450

Gnomad OTH

AF:

0.0201

GnomAD4 exome

AF:

0.0756

AC:

AN:

516

Hom.:

Cov.:

AF XY:

0.0693

AC XY:

AN XY:

332

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.0829

AC:

AN:

434

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0500

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0304

AC:

4623

AN:

152150

Hom.:

112

Cov.:

AF XY:

0.0310

AC XY:

2309

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.00725

AC:

301

AN:

41516

American (AMR)

AF:

0.0181

AC:

277

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0150

AC:

AN:

3472

East Asian (EAS)

AF:

0.000386

AC:

AN:

5176

South Asian (SAS)

AF:

0.00663

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.0803

AC:

846

AN:

10540

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0450

AC:

3063

AN:

68016

Other (OTH)

AF:

0.0199

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

223

446

670

893

1116

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

192

256

320

<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:

0.0375

Hom.:

Bravo

AF:

0.0245

Asia WGS

AF:

0.00606

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.17

(source)

DANN

Benign

0.59

PhyloP100

-1.4

Mutation Taster

=100/0

polymorphism

(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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over