chr3-42087337-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000673621.2(TRAK1):c.112A>G(p.Ile38Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000723 in 152,242 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000673621.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAK1 | NM_001349245.1 | c.-285A>G | 5_prime_UTR_variant | 1/16 | |||
TRAK1 | XM_017005909.2 | c.-285A>G | 5_prime_UTR_variant | 2/17 | |||
TRAK1 | XM_017005911.2 | c.-285A>G | 5_prime_UTR_variant | 2/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAK1 | ENST00000673621.2 | c.112A>G | p.Ile38Val | missense_variant | 2/17 | ||||
TRAK1 | ENST00000484786.5 | c.-285A>G | 5_prime_UTR_variant | 1/13 | 5 | ||||
TRAK1 | ENST00000487159.5 | c.-285A>G | 5_prime_UTR_variant | 2/17 | 5 | ||||
TRAK1 | ENST00000672026.1 | c.-285A>G | 5_prime_UTR_variant | 2/18 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152242Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 584Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 376
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74382
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2022 | TRAK1: PM2, BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at