Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP6_Very_StrongBP7
The NM_001244008.2(KIF1A):c.2070G>A(p.Arg690Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000166 in 1,448,596 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
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]
Our verdict: Benign. The variant received -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
Variant 2-240762765-C-T is Benign according to our data. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240762765-C-T is described in CliVar as Likely_benign. Clinvar id is 532878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.523 with no splicing effect.
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. -