2-240775931-G-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_001244008.2(KIF1A):c.883-5C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00013 in 1,599,922 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001244008.2 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000473 AC: 72AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000137 AC: 34AN: 248800Hom.: 0 AF XY: 0.0000962 AC XY: 13AN XY: 135086
GnomAD4 exome AF: 0.0000939 AC: 136AN: 1447586Hom.: 1 Cov.: 27 AF XY: 0.0000874 AC XY: 63AN XY: 721068
GnomAD4 genome AF: 0.000473 AC: 72AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.000470 AC XY: 35AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:4
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KIF1A: BP4 -
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Inborn genetic diseases Benign:1
This alteration is classified as likely 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. -
KIF1A-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Neuropathy, hereditary sensory, type 2C;C5235139:Hereditary spastic paraplegia 30;C5393830:Intellectual disability, autosomal dominant 9 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at