rs375180690
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS1
The NM_001244008.2(KIF1A):c.1437C>T(p.Ala479Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000362 in 1,609,758 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001244008.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000381 AC: 58AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000448 AC: 108AN: 240952Hom.: 0 AF XY: 0.000465 AC XY: 61AN XY: 131080
GnomAD4 exome AF: 0.000360 AC: 524AN: 1457394Hom.: 0 Cov.: 31 AF XY: 0.000385 AC XY: 279AN XY: 724568
GnomAD4 genome AF: 0.000381 AC: 58AN: 152364Hom.: 0 Cov.: 33 AF XY: 0.000403 AC XY: 30AN XY: 74510
ClinVar
Submissions by phenotype
not provided Benign:4
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KIF1A: BP4, BP7 -
Hereditary spastic paraplegia 30 Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
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. -
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