Variant chr1-10232301-C-CAT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_001365951.3(KIF1B):c.-16_-15dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00241 in 1,429,268 control chromosomes in the GnomAD database, including 15 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0062 ( 7 hom., cov: 31)

Exomes 𝑓: 0.0020 ( 8 hom. )

Consequence

KIF1B
NM_001365951.3 5_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:3

Conservation

PhyloP100: 0.439

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 -10 ACMG points.

BP6

Variant 1-10232301-C-CAT is Benign according to our data. Variant chr1-10232301-C-CAT is described in ClinVar as [Likely_benign]. Clinvar id is 291463.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00619 (937/151448) while in subpopulation AFR AF= 0.0175 (722/41336). AF 95% confidence interval is 0.0164. There are 7 homozygotes in gnomad4. There are 447 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High AC in GnomAd4 at 937 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF1B	NM_001365951.3 linkuse as main transcript	c.-16_-15dup		5_prime_UTR_variant	2/49	ENST00000676179.1	NP_001352880.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF1B	ENST00000676179.1 linkuse as main transcript	c.-16_-15dup		5_prime_UTR_variant	2/49		NM_001365951.3	ENSP00000502065	P1	O60333-1

Frequencies

GnomAD3 genomes

AF:

0.00615

AC:

931

AN:

151332

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0174

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00390

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.0125

Gnomad SAS

AF:

0.00146

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000944

Gnomad OTH

AF:

0.00724

GnomAD3 exomes

AF:

0.00361

AC:

695

AN:

192740

Hom.:

AF XY:

0.00301

AC XY:

310

AN XY:

103150

show subpopulations

Gnomad AFR exome

AF:

0.0191

Gnomad AMR exome

AF:

0.00236

Gnomad ASJ exome

AF:

0.000480

Gnomad EAS exome

AF:

0.0136

Gnomad SAS exome

AF:

0.00233

Gnomad FIN exome

AF:

0.000185

Gnomad NFE exome

AF:

0.00135

Gnomad OTH exome

AF:

0.00395

GnomAD4 exome

AF:

0.00197

AC:

2514

AN:

1277820

Hom.:

Cov.:

AF XY:

0.00189

AC XY:

1217

AN XY:

642358

show subpopulations

Gnomad4 AFR exome

AF:

0.0165

Gnomad4 AMR exome

AF:

0.00213

Gnomad4 ASJ exome

AF:

0.000530

Gnomad4 EAS exome

AF:

0.00866

Gnomad4 SAS exome

AF:

0.00203

Gnomad4 FIN exome

AF:

0.000135

Gnomad4 NFE exome

AF:

0.00125

Gnomad4 OTH exome

AF:

0.00345

GnomAD4 genome

AF:

0.00619

AC:

937

AN:

151448

Hom.:

Cov.:

AF XY:

0.00604

AC XY:

447

AN XY:

73990

show subpopulations

Gnomad4 AFR

AF:

0.0175

Gnomad4 AMR

AF:

0.00389

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.0126

Gnomad4 SAS

AF:

0.00146

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000944

Gnomad4 OTH

AF:

0.00764

Bravo

AF:

0.00678

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Neuroblastoma

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Pheochromocytoma

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Charcot-Marie-Tooth disease type 2

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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