Variant 21-44133763-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_004649.8(GATD3):c.66C>G(p.Ser22=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0031 ( 32 hom., cov: 1)

Exomes 𝑓: 0.00061 ( 89 hom. )

Failed GnomAD Quality Control

Consequence

GATD3
NM_004649.8 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.29

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 21-44133763-C-G is Benign according to our data. Variant chr21-44133763-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2652731.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-3.29 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 89 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GATD3	NM_004649.8 linkuse as main transcript	c.66C>G	p.Ser22=	synonymous_variant	1/7	ENST00000291577.11	NP_004640.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GATD3	ENST00000291577.11 linkuse as main transcript	c.66C>G	p.Ser22=	synonymous_variant	1/7	1	NM_004649.8	ENSP00000291577	P1	P0DPI2-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

182

AN:

59908

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00634

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000936

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00105

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000102

Gnomad OTH

AF:

0.00529

GnomAD3 exomes

AF:

0.000427

AC:

AN:

194408

Hom.:

AF XY:

0.000323

AC XY:

AN XY:

105190

show subpopulations

Gnomad AFR exome

AF:

0.00541

Gnomad AMR exome

AF:

0.000512

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0000684

Gnomad NFE exome

AF:

0.0000237

Gnomad OTH exome

AF:

0.000198

GnomAD4 exome

AF:

0.000612

AC:

296

AN:

483388

Hom.:

Cov.:

AF XY:

0.000545

AC XY:

134

AN XY:

245860

show subpopulations

Gnomad4 AFR exome

AF:

0.00756

Gnomad4 AMR exome

AF:

0.00176

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00150

Gnomad4 NFE exome

AF:

0.0000371

Gnomad4 OTH exome

AF:

0.00148

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00308

AC:

185

AN:

59998

Hom.:

Cov.:

AF XY:

0.00310

AC XY:

AN XY:

28702

show subpopulations

Gnomad4 AFR

AF:

0.00643

Gnomad4 AMR

AF:

0.000935

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00105

Gnomad4 NFE

AF:

0.000102

Gnomad4 OTH

AF:

0.00515

Alfa

AF:

0.000587

Hom.:

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2022

GATD3: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

3.6

DANN

Benign

0.55

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over