dbSNP rs7282490: GATD3:c.312-12055G>A (chr21-44195858-G-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000646873.1(GATD3):c.312-12055G>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 0.0 ( 0 hom., cov: 10)

Failed GnomAD Quality Control

Consequence

GATD3
ENST00000646873.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.41

Publications

58 publications found

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]

GATD3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
GATD3	ENST00000646873.1 link	c.312-12055G>A	intron_variant	Intron 3 of 4	ENSP00000494853.1	A0A2R8YDR7
GATD3	ENST00000644251.1 link	c.429-6192G>A	intron_variant	Intron 4 of 4	ENSP00000495305.1	A0A2R8Y6K9
GATD3	ENST00000645487.1 link	n.*202-1313G>A	intron_variant	Intron 3 of 3	ENSP00000494347.1	A0A2R8Y588

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

78024

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

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: AC0

AF:

0.00

AC:

AN:

78024

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

37924

African (AFR)

AF:

0.00

AC:

AN:

9870

American (AMR)

AF:

0.00

AC:

AN:

10766

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2112

East Asian (EAS)

AF:

0.00

AC:

AN:

3506

South Asian (SAS)

AF:

0.00

AC:

AN:

2334

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6322

Middle Eastern (MID)

AF:

0.00

AC:

AN:

156

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

41266

Other (OTH)

AF:

0.00

AC:

AN:

1044

Alfa

AF:

0.598

Hom.:

89031

Asia WGS

AF:

0.562

AC:

1956

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.7

(source)

DANN

Benign

0.78

PhyloP100

-2.4

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over