rs2838513
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000449622.6(GATD3):c.490-18133G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0014 ( 1 hom., cov: 10)
Failed GnomAD Quality Control
Consequence
GATD3
ENST00000449622.6 intron
ENST00000449622.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.05
Genes affected
GATD3 (HGNC:1273): (glutamine amidotransferase class 1 domain containing 3) This gene encodes a potential mitochondrial protein that is a member of the DJ-1/PfpI gene family. This protein is overexpressed in fetal Down syndrome brain. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOC105377139 | XR_001755082.3 | n.569-339C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GATD3 | ENST00000646873.1 | c.312-32422G>A | intron_variant | ENSP00000494853.1 | ||||||
GATD3 | ENST00000449622.6 | c.490-18133G>A | intron_variant | 2 | ENSP00000400044.2 | |||||
GATD3 | ENST00000644251.1 | c.429-26559G>A | intron_variant | ENSP00000495305.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 106AN: 76040Hom.: 0 Cov.: 10 FAILED QC
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00144 AC: 110AN: 76144Hom.: 1 Cov.: 10 AF XY: 0.00148 AC XY: 55AN XY: 37084
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
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76144
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at