rs10492969

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001365951.3(KIF1B):​c.-79-5950T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 152,044 control chromosomes in the GnomAD database, including 23,903 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 0.55 ( 23903 hom., cov: 31)

Consequence

KIF1B
NM_001365951.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.20
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KIF1BNM_001365951.3 linkuse as main transcriptc.-79-5950T>C intron_variant ENST00000676179.1 NP_001352880.1
KIF1BNM_001365952.1 linkuse as main transcriptc.-79-5950T>C intron_variant NP_001352881.1
KIF1BNM_015074.3 linkuse as main transcriptc.-79-5950T>C intron_variant NP_055889.2
KIF1BNM_183416.4 linkuse as main transcriptc.-79-5950T>C intron_variant NP_904325.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KIF1BENST00000676179.1 linkuse as main transcriptc.-79-5950T>C intron_variant NM_001365951.3 ENSP00000502065 P1O60333-1

Frequencies

GnomAD3 genomes
AF:
0.548
AC:
83242
AN:
151926
Hom.:
23857
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.725
Gnomad AMI
AF:
0.558
Gnomad AMR
AF:
0.510
Gnomad ASJ
AF:
0.546
Gnomad EAS
AF:
0.366
Gnomad SAS
AF:
0.446
Gnomad FIN
AF:
0.499
Gnomad MID
AF:
0.544
Gnomad NFE
AF:
0.478
Gnomad OTH
AF:
0.536
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.548
AC:
83350
AN:
152044
Hom.:
23903
Cov.:
31
AF XY:
0.546
AC XY:
40568
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.725
Gnomad4 AMR
AF:
0.511
Gnomad4 ASJ
AF:
0.546
Gnomad4 EAS
AF:
0.366
Gnomad4 SAS
AF:
0.445
Gnomad4 FIN
AF:
0.499
Gnomad4 NFE
AF:
0.478
Gnomad4 OTH
AF:
0.539
Alfa
AF:
0.488
Hom.:
26176
Bravo
AF:
0.558
Asia WGS
AF:
0.459
AC:
1595
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.24
DANN
Benign
0.48

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.

Other links and lift over

dbSNP: rs10492969; hg19: chr1-10286358; API