1-10268280-C-T

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001365951.3(KIF1B):c.720+17C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 1,493,890 control chromosomes in the GnomAD database, including 63,411 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5373 hom., cov: 31)

Exomes 𝑓: 0.29 ( 58038 hom. )

Consequence

KIF1B
NM_001365951.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: -1.56

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 1-10268280-C-T is Benign according to our data. Variant chr1-10268280-C-T is described in ClinVar as [Benign]. Clinvar id is 260542.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-10268280-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF1B	NM_001365951.3 link	c.720+17C>T		intron_variant	Intron 7 of 48	ENST00000676179.1	NP_001352880.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF1B	ENST00000676179.1 link	c.720+17C>T		intron_variant	Intron 7 of 48		NM_001365951.3	ENSP00000502065.1		O60333-1

Frequencies

GnomAD3 genomes

AF:

0.257

AC:

38990

AN:

151908

Hom.:

5356

Cov.:

show subpopulations

Gnomad AFR

AF:

0.158

Gnomad AMI

AF:

0.363

Gnomad AMR

AF:

0.320

Gnomad ASJ

AF:

0.266

Gnomad EAS

AF:

0.285

Gnomad SAS

AF:

0.240

Gnomad FIN

AF:

0.293

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.294

Gnomad OTH

AF:

0.267

GnomAD3 exomes

AF:

0.282

AC:

70135

AN:

248986

Hom.:

10137

AF XY:

0.279

AC XY:

37491

AN XY:

134552

show subpopulations

Gnomad AFR exome

AF:

0.153

Gnomad AMR exome

AF:

0.349

Gnomad ASJ exome

AF:

0.270

Gnomad EAS exome

AF:

0.291

Gnomad SAS exome

AF:

0.230

Gnomad FIN exome

AF:

0.293

Gnomad NFE exome

AF:

0.292

Gnomad OTH exome

AF:

0.269

GnomAD4 exome

AF:

0.292

AC:

391352

AN:

1341862

Hom.:

58038

Cov.:

AF XY:

0.290

AC XY:

195281

AN XY:

673870

show subpopulations

Gnomad4 AFR exome

AF:

0.149

Gnomad4 AMR exome

AF:

0.341

Gnomad4 ASJ exome

AF:

0.272

Gnomad4 EAS exome

AF:

0.256

Gnomad4 SAS exome

AF:

0.226

Gnomad4 FIN exome

AF:

0.301

Gnomad4 NFE exome

AF:

0.302

Gnomad4 OTH exome

AF:

0.285

GnomAD4 genome

AF:

0.257

AC:

39040

AN:

152028

Hom.:

5373

Cov.:

AF XY:

0.258

AC XY:

19141

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.158

Gnomad4 AMR

AF:

0.321

Gnomad4 ASJ

AF:

0.266

Gnomad4 EAS

AF:

0.285

Gnomad4 SAS

AF:

0.240

Gnomad4 FIN

AF:

0.293

Gnomad4 NFE

AF:

0.294

Gnomad4 OTH

AF:

0.272

Alfa

AF:

0.242

Hom.:

1521

Bravo

AF:

0.257

Asia WGS

AF:

0.275

AC:

955

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Clinical Genetics, Academic Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jul 28, 2020

Ambry Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Charcot-Marie-Tooth disease

Benign:1

Molecular Genetics Laboratory, London Health Sciences Centre

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Pheochromocytoma

Benign:1

Aug 19, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Charcot-Marie-Tooth disease type 2

Benign:1

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Charcot-Marie-Tooth disease type 2A1

Benign:1

Aug 19, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

3.5

DANN

Benign

0.57

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over