rs762421
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000646873.1(GATD3):c.313-12235G>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 0.0013 ( 22 hom., cov: 9)
Failed GnomAD Quality Control
Consequence
GATD3
ENST00000646873.1 intron
ENST00000646873.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.336
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=-1.02).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATD3 | ENST00000644251.1 | c.429-6372G>A | intron_variant | ||||||
GATD3 | ENST00000646873.1 | c.313-12235G>A | intron_variant | ||||||
GATD3 | ENST00000645487.1 | c.*202-1493G>A | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 98AN: 75414Hom.: 21 Cov.: 9 FAILED QC
GnomAD3 genomes
?
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98
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75414
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9
FAILED QC
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.00134 AC: 101AN: 75440Hom.: 22 Cov.: 9 AF XY: 0.00107 AC XY: 39AN XY: 36562
GnomAD4 genome
?
Data not reliable, filtered out with message: AS_VQSR
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101
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75440
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9
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39
AN XY:
36562
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2237
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3478
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