rs10634555
Positions:
- chr3-42210085-CGGAGGAGGAGGAGGA-C
- chr3-42210085-CGGAGGAGGAGGAGGA-CGGA
- chr3-42210085-CGGAGGAGGAGGAGGA-CGGAGGA
- chr3-42210085-CGGAGGAGGAGGAGGA-CGGAGGAGGA
- chr3-42210085-CGGAGGAGGAGGAGGA-CGGAGGAGGAGGA
- chr3-42210085-CGGAGGAGGAGGAGGA-CGGAGGAGGAGGAGGAGGA
- chr3-42210085-CGGAGGAGGAGGAGGA-CGGAGGAGGAGGAGGAGGAGGA
- chr3-42210085-CGGAGGAGGAGGAGGA-CGGAGGAGGAGGAGGAGGAGGAGGA
- chr3-42210085-CGGAGGAGGAGGAGGA-CGGAGGAGGAGGAGGAGGAGGAGGAGGA
- chr3-42210085-CGGAGGAGGAGGAGGA-CGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3
The ENST00000341421.7(TRAK1):c.1907_1921del(p.Glu636_Glu640del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,577,352 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000019 ( 0 hom. )
Consequence
TRAK1
ENST00000341421.7 inframe_deletion
ENST00000341421.7 inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.53
Genes affected
TRAK1 (HGNC:29947): (trafficking kinesin protein 1) Predicted to enable GABA receptor binding activity and myosin binding activity. Involved in endosome to lysosome transport. Located in early endosome and mitochondrion. Implicated in developmental and epileptic encephalopathy 68. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP3
Nonframeshift variant in repetitive region in ENST00000341421.7
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRAK1 | NM_001042646.3 | c.1963+118_1963+132del | intron_variant | ENST00000327628.10 | NP_001036111.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRAK1 | ENST00000327628.10 | c.1963+118_1963+132del | intron_variant | 1 | NM_001042646.3 | ENSP00000328998 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000122 AC: 18AN: 147430Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.0000189 AC: 27AN: 1429922Hom.: 0 AF XY: 0.0000183 AC XY: 13AN XY: 710170
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GnomAD4 genome AF: 0.000122 AC: 18AN: 147430Hom.: 0 Cov.: 0 AF XY: 0.000154 AC XY: 11AN XY: 71516
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at