1-10268280-C-T
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
Consequence
NM_001365951.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF1B | NM_001365951.3 | c.720+17C>T | intron_variant | Intron 7 of 48 | ENST00000676179.1 | NP_001352880.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.257 AC: 38990AN: 151908Hom.: 5356 Cov.: 31
GnomAD3 exomes AF: 0.282 AC: 70135AN: 248986Hom.: 10137 AF XY: 0.279 AC XY: 37491AN XY: 134552
GnomAD4 exome AF: 0.292 AC: 391352AN: 1341862Hom.: 58038 Cov.: 20 AF XY: 0.290 AC XY: 195281AN XY: 673870
GnomAD4 genome AF: 0.257 AC: 39040AN: 152028Hom.: 5373 Cov.: 31 AF XY: 0.258 AC XY: 19141AN XY: 74300
ClinVar
Submissions by phenotype
not specified Benign:4
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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. -
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not provided Benign:2
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Charcot-Marie-Tooth disease Benign:1
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Pheochromocytoma Benign:1
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Charcot-Marie-Tooth disease type 2 Benign:1
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Charcot-Marie-Tooth disease type 2A1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at