1-10210698-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001365951.3(KIF1B):c.-260C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0018 in 151,528 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0018 ( 2 hom., cov: 32)
Exomes 𝑓: 0.015 ( 0 hom. )
Consequence
KIF1B
NM_001365951.3 5_prime_UTR
NM_001365951.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.25
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant 1-10210698-C-T is Benign according to our data. Variant chr1-10210698-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 368793.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 269 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF1B | NM_001365951.3 | c.-260C>T | 5_prime_UTR_variant | Exon 1 of 49 | ENST00000676179.1 | NP_001352880.1 | ||
KIF1B | NM_183416.4 | c.-260C>T | 5_prime_UTR_variant | Exon 1 of 21 | NP_904325.2 | |||
KIF1B | NM_015074.3 | c.-260C>T | upstream_gene_variant | NP_055889.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF1B | ENST00000676179 | c.-260C>T | 5_prime_UTR_variant | Exon 1 of 49 | NM_001365951.3 | ENSP00000502065.1 | ||||
KIF1B | ENST00000377093 | c.-260C>T | 5_prime_UTR_variant | Exon 1 of 21 | 1 | ENSP00000366297.4 | ||||
KIF1B | ENST00000696500.1 | n.-260C>T | non_coding_transcript_exon_variant | Exon 1 of 22 | ENSP00000512666.1 | |||||
KIF1B | ENST00000696500.1 | n.-260C>T | 5_prime_UTR_variant | Exon 1 of 22 | ENSP00000512666.1 |
Frequencies
GnomAD3 genomes AF: 0.00178 AC: 269AN: 151218Hom.: 2 Cov.: 32
GnomAD3 genomes
AF:
AC:
269
AN:
151218
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0147 AC: 3AN: 204Hom.: 0 AF XY: 0.0197 AC XY: 3AN XY: 152
GnomAD4 exome
AF:
AC:
3
AN:
204
Hom.:
AF XY:
AC XY:
3
AN XY:
152
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00178 AC: 269AN: 151324Hom.: 2 Cov.: 32 AF XY: 0.00185 AC XY: 137AN XY: 73958
GnomAD4 genome
AF:
AC:
269
AN:
151324
Hom.:
Cov.:
32
AF XY:
AC XY:
137
AN XY:
73958
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
10
AN:
3362
ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Pheochromocytoma Benign:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Neuroblastoma Benign:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Charcot-Marie-Tooth disease type 2 Benign:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at