Genetic Variant KIF1B:p.Ala95Ala (chr1-10258594-C-G) – ACMG Classification: Benign (-19 pts)

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001365951.3(KIF1B):c.285C>G(p.Ala95Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 1,613,504 control chromosomes in the GnomAD database, including 67,279 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. A95A) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.24 ( 4968 hom., cov: 32)

Exomes 𝑓: 0.29 ( 62311 hom. )

Consequence

KIF1B
NM_001365951.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:13

Conservation

PhyloP100: 0.0670

Publications

26 publications found

Variant links:

Genes affected

KIF1B (HGNC:16636): (kinesin family member 1B) Predicted to enable microtubule binding activity and plus-end-directed microtubule motor activity. Predicted to be involved in chemical synaptic transmission; dense core granule cytoskeletal transport; and vesicle-mediated transport. Predicted to act upstream of or within mitochondrion transport along microtubule. Predicted to be located in cytoplasmic vesicle membrane and neuron projection. Predicted to be part of kinesin complex. Predicted to be active in several cellular components, including axon; dendrite; and microtubule. Implicated in Charcot-Marie-Tooth disease type 2A1; carcinoma (multiple); multiple sclerosis; neuroblastoma; and pheochromocytoma. Biomarker of hepatocellular carcinoma. [provided by Alliance of Genome Resources, Apr 2022]

KIF1B Gene-Disease associations (from GenCC):

pheochromocytoma
Inheritance: AD Classification: MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
Charcot-Marie-Tooth disease type 2A1
Inheritance: AD Classification: SUPPORTIVE, LIMITED, NO_KNOWN Submitted by: ClinGen, Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae)
hereditary pheochromocytoma-paraganglioma
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
neuroblastoma, susceptibility to, 1
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

KIF1B links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BP6

Variant 1-10258594-C-G is Benign according to our data. Variant chr1-10258594-C-G is described in ClinVar as Benign. ClinVar VariationId is 129399.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.067 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001365951.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
KIF1B	NM_001365951.3	MANE Select	c.285C>G	p.Ala95Ala	synonymous	Exon 4 of 49	NP_001352880.1	O60333-1
KIF1B	NM_001365952.1		c.285C>G	p.Ala95Ala	synonymous	Exon 4 of 49	NP_001352881.1	O60333-1
KIF1B	NM_015074.3		c.285C>G	p.Ala95Ala	synonymous	Exon 4 of 47	NP_055889.2	O60333-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
KIF1B	ENST00000676179.1	MANE Select	c.285C>G	p.Ala95Ala	synonymous	Exon 4 of 49	ENSP00000502065.1	O60333-1
KIF1B	ENST00000377081.5	TSL:1	c.285C>G	p.Ala95Ala	synonymous	Exon 3 of 48	ENSP00000366284.1	O60333-4
KIF1B	ENST00000377086.5	TSL:1	c.285C>G	p.Ala95Ala	synonymous	Exon 4 of 49	ENSP00000366290.1	O60333-1

Frequencies

GnomAD3 genomes

AF:

0.237

AC:

36045

AN:

151954

Hom.:

4955

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0922

Gnomad AMI

AF:

0.365

Gnomad AMR

AF:

0.310

Gnomad ASJ

AF:

0.266

Gnomad EAS

AF:

0.283

Gnomad SAS

AF:

0.240

Gnomad FIN

AF:

0.291

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.294

Gnomad OTH

AF:

0.254

GnomAD2 exomes

AF:

0.277

AC:

69540

AN:

251442

AF XY:

0.275

show subpopulations

Gnomad AFR exome

AF:

0.0864

Gnomad AMR exome

AF:

0.345

Gnomad ASJ exome

AF:

0.269

Gnomad EAS exome

AF:

0.292

Gnomad FIN exome

AF:

0.293

Gnomad NFE exome

AF:

0.291

Gnomad OTH exome

AF:

0.265

GnomAD4 exome

AF:

0.289

AC:

422278

AN:

1461432

Hom.:

62311

Cov.:

AF XY:

0.288

AC XY:

209040

AN XY:

727048

show subpopulations

African (AFR)

AF:

0.0806

AC:

2698

AN:

33476

American (AMR)

AF:

0.337

AC:

15052

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.271

AC:

7072

AN:

26132

East Asian (EAS)

AF:

0.256

AC:

10173

AN:

39688

South Asian (SAS)

AF:

0.226

AC:

19465

AN:

86250

European-Finnish (FIN)

AF:

0.301

AC:

16083

AN:

53416

Middle Eastern (MID)

AF:

0.201

AC:

1157

AN:

5768

European-Non Finnish (NFE)

AF:

0.300

AC:

333614

AN:

1111596

Other (OTH)

AF:

0.281

AC:

16964

AN:

60382

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

15741

31482

47223

62964

78705

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10902

21804

32706

43608

54510

<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:

0.237

AC:

36076

AN:

152072

Hom.:

4968

Cov.:

AF XY:

0.238

AC XY:

17697

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.0921

AC:

3824

AN:

41498

American (AMR)

AF:

0.311

AC:

4740

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.266

AC:

923

AN:

3472

East Asian (EAS)

AF:

0.283

AC:

1465

AN:

5174

South Asian (SAS)

AF:

0.239

AC:

1153

AN:

4818

European-Finnish (FIN)

AF:

0.291

AC:

3067

AN:

10542

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.294

AC:

19964

AN:

67990

Other (OTH)

AF:

0.259

AC:

547

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1351

2702

4054

5405

6756

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

368

736

1104

1472

1840

<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:

0.240

Hom.:

1541

Bravo

AF:

0.235

EpiCase

AF:

0.294

EpiControl

AF:

0.295

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (6)

not provided (2)

Charcot-Marie-Tooth disease (1)

Charcot-Marie-Tooth disease type 2 (1)

Charcot-Marie-Tooth disease type 2A1 (1)

Neuroblastoma (1)

Pheochromocytoma (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

(source)

DANN

Benign

0.68

PhyloP100

0.067

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=89/11

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