chr2-240763268-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_001244008.2(KIF1A):c.1847C>T(p.Thr616Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000577 in 1,611,244 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. T616T) has been classified as Likely benign.
Frequency
Consequence
NM_001244008.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF1A | NM_001244008.2 | c.1847C>T | p.Thr616Met | missense_variant | 21/49 | ENST00000498729.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF1A | ENST00000498729.9 | c.1847C>T | p.Thr616Met | missense_variant | 21/49 | 5 | NM_001244008.2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152260Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000663 AC: 16AN: 241250Hom.: 0 AF XY: 0.0000608 AC XY: 8AN XY: 131562
GnomAD4 exome AF: 0.0000569 AC: 83AN: 1458866Hom.: 1 Cov.: 35 AF XY: 0.0000689 AC XY: 50AN XY: 725496
GnomAD4 genome AF: 0.0000656 AC: 10AN: 152378Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74516
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Feb 13, 2023 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2018 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 02, 2022 | The p.T616M variant (also known as c.1847C>T), located in coding exon 20 of the KIF1A gene, results from a C to T substitution at nucleotide position 1847. The threonine at codon 616 is replaced by methionine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Hereditary spastic paraplegia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Oct 02, 2017 | - - |
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 | Nov 21, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at