chr3-42125451-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001042646.3(TRAK1):c.123C>T(p.Val41=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00366 in 1,614,130 control chromosomes in the GnomAD database, including 104 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0028 ( 5 hom., cov: 32)
Exomes 𝑓: 0.0038 ( 99 hom. )
Consequence
TRAK1
NM_001042646.3 synonymous
NM_001042646.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.701
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 Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
?
Variant 3-42125451-C-T is Benign according to our data. Variant chr3-42125451-C-T is described in ClinVar as [Benign]. Clinvar id is 1600230.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-42125451-C-T is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.701 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00275 (419/152276) while in subpopulation SAS AF= 0.0383 (185/4824). AF 95% confidence interval is 0.0338. There are 5 homozygotes in gnomad4. There are 229 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAK1 | NM_001042646.3 | c.123C>T | p.Val41= | synonymous_variant | 2/16 | ENST00000327628.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAK1 | ENST00000327628.10 | c.123C>T | p.Val41= | synonymous_variant | 2/16 | 1 | NM_001042646.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00275 AC: 419AN: 152156Hom.: 5 Cov.: 32
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GnomAD3 exomes AF: 0.00624 AC: 1557AN: 249354Hom.: 35 AF XY: 0.00799 AC XY: 1081AN XY: 135264
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GnomAD4 exome AF: 0.00375 AC: 5488AN: 1461854Hom.: 99 Cov.: 31 AF XY: 0.00492 AC XY: 3578AN XY: 727232
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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 | Invitae | Jan 06, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at