2-240746109-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6BP7
The NM_001244008.2(KIF1A):c.3132C>T(p.Ile1044=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000234 in 1,582,944 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). Synonymous variant affecting the same amino acid position (i.e. I1044I) has been classified as Likely benign.
Frequency
Consequence
NM_001244008.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF1A | NM_001244008.2 | c.3132C>T | p.Ile1044= | synonymous_variant | 30/49 | ENST00000498729.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF1A | ENST00000498729.9 | c.3132C>T | p.Ile1044= | synonymous_variant | 30/49 | 5 | NM_001244008.2 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000204 AC: 4AN: 195950Hom.: 0 AF XY: 0.00000944 AC XY: 1AN XY: 105938
GnomAD4 exome AF: 0.0000126 AC: 18AN: 1430736Hom.: 0 Cov.: 33 AF XY: 0.0000113 AC XY: 8AN XY: 708930
GnomAD4 genome AF: 0.000125 AC: 19AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74354
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Nov 01, 2018 | - - |
Neuropathy, hereditary sensory, type 2C;C5235139:Hereditary spastic paraplegia 30;C5393830:Intellectual disability, autosomal dominant 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 07, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at