dbSNP rs11121552: KIF1B:p.Thr1767Thr (chr1-10375266-C-A) – 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.5301C>A(p.Thr1767Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 1,611,190 control chromosomes in the GnomAD database, including 69,030 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. T1767T) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.24 ( 5109 hom., cov: 32)

Exomes 𝑓: 0.29 ( 63921 hom. )

Consequence

KIF1B
NM_001365951.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.590

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:

Genome browser will be placed here

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=-0.25).

BP6

Variant 1-10375266-C-A is Benign according to our data. Variant chr1-10375266-C-A is described in ClinVar as Benign. ClinVar VariationId is 129401.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.59 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.305 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.5301C>A	p.Thr1767Thr	synonymous	Exon 48 of 49	NP_001352880.1	O60333-1
KIF1B	NM_001365952.1		c.5301C>A	p.Thr1767Thr	synonymous	Exon 48 of 49	NP_001352881.1	O60333-1
KIF1B	NM_015074.3		c.5163C>A	p.Thr1721Thr	synonymous	Exon 46 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.5301C>A	p.Thr1767Thr	synonymous	Exon 48 of 49	ENSP00000502065.1	O60333-1
KIF1B	ENST00000377081.5	TSL:1	c.5301C>A	p.Thr1767Thr	synonymous	Exon 47 of 48	ENSP00000366284.1	O60333-4
KIF1B	ENST00000377086.5	TSL:1	c.5301C>A	p.Thr1767Thr	synonymous	Exon 48 of 49	ENSP00000366290.1	O60333-1

Frequencies

GnomAD3 genomes

AF:

0.240

AC:

36524

AN:

152076

Hom.:

5097

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0929

Gnomad AMI

AF:

0.431

Gnomad AMR

AF:

0.312

Gnomad ASJ

AF:

0.267

Gnomad EAS

AF:

0.277

Gnomad SAS

AF:

0.250

Gnomad FIN

AF:

0.295

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.298

Gnomad OTH

AF:

0.256

GnomAD2 exomes

AF:

0.280

AC:

70290

AN:

251460

AF XY:

0.278

show subpopulations

Gnomad AFR exome

AF:

0.0874

Gnomad AMR exome

AF:

0.346

Gnomad ASJ exome

AF:

0.271

Gnomad EAS exome

AF:

0.285

Gnomad FIN exome

AF:

0.295

Gnomad NFE exome

AF:

0.296

Gnomad OTH exome

AF:

0.268

GnomAD4 exome

AF:

0.292

AC:

426426

AN:

1458996

Hom.:

63921

Cov.:

AF XY:

0.291

AC XY:

211236

AN XY:

725932

show subpopulations

African (AFR)

AF:

0.0812

AC:

2716

AN:

33456

American (AMR)

AF:

0.338

AC:

15125

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.272

AC:

7094

AN:

26120

East Asian (EAS)

AF:

0.251

AC:

9974

AN:

39688

South Asian (SAS)

AF:

0.233

AC:

20104

AN:

86182

European-Finnish (FIN)

AF:

0.303

AC:

16185

AN:

53412

Middle Eastern (MID)

AF:

0.201

AC:

1157

AN:

5742

European-Non Finnish (NFE)

AF:

0.304

AC:

336988

AN:

1109372

Other (OTH)

AF:

0.283

AC:

17083

AN:

60300

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.449

Heterozygous variant carriers

15386

30771

46157

61542

76928

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10964

21928

32892

43856

54820

<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:

0.240

AC:

36555

AN:

152194

Hom.:

5109

Cov.:

AF XY:

0.241

AC XY:

17959

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.0929

AC:

3859

AN:

41548

American (AMR)

AF:

0.313

AC:

4782

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.267

AC:

926

AN:

3472

East Asian (EAS)

AF:

0.276

AC:

1431

AN:

5178

South Asian (SAS)

AF:

0.250

AC:

1209

AN:

4828

European-Finnish (FIN)

AF:

0.295

AC:

3118

AN:

10584

Middle Eastern (MID)

AF:

0.211

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.298

AC:

20231

AN:

67990

Other (OTH)

AF:

0.259

AC:

547

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1405

2810

4216

5621

7026

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

370

740

1110

1480

1850

<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:

0.268

Hom.:

3272

Bravo

AF:

0.237

Asia WGS

AF:

0.272

AC:

943

AN:

3478

EpiCase

AF:

0.298

EpiControl

AF:

0.299

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

-0.25

CADD

Benign

5.7

(source)

DANN

Benign

0.74

PhyloP100

-0.59

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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