21-44143322-C-T

Variant names:

• chr21-44143322-C-T
• rs752956051
• NM_004649.8:c.639C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4 BP7

The NM_004649.8(GATD3):​c.639C>T​(p.Ile213Ile) variant causes a synonymous 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: not found (cov: 0)
• Consequence: GATD3 NM_004649.8 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.42
• Publications: 1 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 -2 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.209).
• BP7: Synonymous conserved (PhyloP=2.42 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004649.8. 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
	GATD3	NM_004649.8	MANE Select	c.639C>T	p.Ile213Ile	synonymous	Exon 6 of 7	NP_004640.4	P0DPI2-1
	GATD3	NM_198155.5		c.546C>T	p.Ile182Ile	synonymous	Exon 5 of 6	NP_937798.4	P0DPI2-2
	GATD3	NR_135220.2		n.601C>T		non_coding_transcript_exon	Exon 5 of 6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATD3	ENST00000291577.11	TSL:1 MANE Select	c.639C>T	p.Ile213Ile	synonymous	Exon 6 of 7	ENSP00000291577.6	P0DPI2-1
	GATD3	ENST00000348499.9	TSL:1	c.546C>T	p.Ile182Ile	synonymous	Exon 5 of 6	ENSP00000344901.5	P0DPI2-2
	GATD3	ENST00000938560.1		c.636C>T	p.Ile212Ile	synonymous	Exon 6 of 7	ENSP00000608619.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	8.9
DANN	Benign	0.86
PhyloP100		2.4

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.12		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs752956051; hg19: chr21-45563204; COSMIC: COSV52391098; COSMIC: COSV52391098;