rs11688298
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001244008.2(KIF1A):c.1949+22A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 1,602,658 control chromosomes in the GnomAD database, including 251,646 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). There are indicators that this mutation may affect the branch point..
Frequency
Genomes: 𝑓 0.59 ( 26823 hom., cov: 35)
Exomes 𝑓: 0.55 ( 224823 hom. )
Consequence
KIF1A
NM_001244008.2 intron
NM_001244008.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.212
Genes affected
KIF1A (HGNC:888): (kinesin family member 1A) The protein encoded by this gene is a member of the kinesin family and functions as an anterograde motor protein that transports membranous organelles along axonal microtubules. Mutations at this locus have been associated with spastic paraplegia-30 and hereditary sensory neuropathy IIC. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Apr 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
This place is a probable branch point but likely benign (scored 0 / 10). Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 2-240763144-T-A is Benign according to our data. Variant chr2-240763144-T-A is described in ClinVar as [Benign]. Clinvar id is 671033.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-240763144-T-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF1A | NM_001244008.2 | c.1949+22A>T | intron_variant | ENST00000498729.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF1A | ENST00000498729.9 | c.1949+22A>T | intron_variant | 5 | NM_001244008.2 |
Frequencies
GnomAD3 genomes AF: 0.588 AC: 89427AN: 152056Hom.: 26804 Cov.: 35
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GnomAD3 exomes AF: 0.531 AC: 125788AN: 236736Hom.: 34477 AF XY: 0.526 AC XY: 68084AN XY: 129380
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GnomAD4 exome AF: 0.553 AC: 802423AN: 1450484Hom.: 224823 Cov.: 40 AF XY: 0.548 AC XY: 395186AN XY: 721182
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GnomAD4 genome AF: 0.588 AC: 89479AN: 152174Hom.: 26823 Cov.: 35 AF XY: 0.582 AC XY: 43327AN XY: 74384
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
BranchPoint Hunter
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at