rs7282490

Variant names:

• chr21-44195858-G-A
• rs7282490
• ENST00000646873.1:c.312-12055G>A

Your query was ambiguous. Multiple possible variants found:

• chr21-44195858-G-A
• chr21-44195858-G-T

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• Publications: 58 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646873.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATD3	ENST00000646873.1		c.312-12055G>A		intron	N/A	ENSP00000494853.1	A0A2R8YDR7
	GATD3	ENST00000644251.1		c.429-6192G>A		intron	N/A	ENSP00000495305.1	A0A2R8Y6K9
	GATD3	ENST00000645487.1		n.*202-1313G>A		intron	N/A	ENSP00000494347.1	A0A2R8Y588

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 78024 Hom.: 0 Cov.: 10

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: 0 AN: 78024 Hom.: 0 Cov.: 10 AF XY: 0.00 AC XY: 0 AN XY: 37924

African (AFR) AF: 0.00 AC: 0 AN: 9870

American (AMR) AF: 0.00 AC: 0 AN: 10766

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2112

East Asian (EAS) AF: 0.00 AC: 0 AN: 3506

South Asian (SAS) AF: 0.00 AC: 0 AN: 2334

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6322

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 156

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 41266

Other (OTH) AF: 0.00 AC: 0 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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.78
PhyloP100		-2.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7282490;

hg19: chr21-45615741;

COSMIC: COSV66846621;

COSMIC: COSV66846621;