rs2838513

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.05
Variant links:
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
LOC105377139XR_001755082.3 linkuse as main transcriptn.569-339C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GATD3ENST00000646873.1 linkuse as main transcriptc.312-32422G>A intron_variant ENSP00000494853.1 A0A2R8YDR7
GATD3ENST00000449622.6 linkuse as main transcriptc.490-18133G>A intron_variant 2 ENSP00000400044.2 H7C1F6
GATD3ENST00000644251.1 linkuse as main transcriptc.429-26559G>A intron_variant ENSP00000495305.1 A0A2R8Y6K9

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
106
AN:
76040
Hom.:
0
Cov.:
10
FAILED QC
Gnomad AFR
AF:
0.00308
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000583
Gnomad ASJ
AF:
0.000585
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000117
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00144
AC:
110
AN:
76144
Hom.:
1
Cov.:
10
AF XY:
0.00148
AC XY:
55
AN XY:
37084
show subpopulations
Gnomad4 AFR
AF:
0.00320
Gnomad4 AMR
AF:
0.000583
Gnomad4 ASJ
AF:
0.000585
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000117
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.230
Hom.:
1495
Asia WGS
AF:
0.606
AC:
2111
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.68
DANN
Benign
0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2838513; hg19: chr21-45595374; API