chr21-44145591-C-A

Variant names:

• chr21-44145591-C-A
• rs7676
• NM_004649.8:c.*642C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_004649.8(GATD3):​c.*642C>A variant causes a 3 prime UTR 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 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76
• Publications: 23 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=0.067).

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.*642C>A		3_prime_UTR	Exon 7 of 7	NP_004640.4	P0DPI2-1
	GATD3	NM_198155.5		c.*642C>A		3_prime_UTR	Exon 6 of 6	NP_937798.4	P0DPI2-2
	GATD3	NR_135220.2		n.1411C>A		non_coding_transcript_exon	Exon 6 of 6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATD3	ENST00000291577.11	TSL:1 MANE Select	c.*642C>A		3_prime_UTR	Exon 7 of 7	ENSP00000291577.6	P0DPI2-1
	GATD3	ENST00000348499.9	TSL:1	c.*642C>A		3_prime_UTR	Exon 6 of 6	ENSP00000344901.5	P0DPI2-2
	GATD3	ENST00000419699.1	TSL:3	c.540C>A	p.Ala180Ala	synonymous	Exon 6 of 6	ENSP00000405713.1	H7C2G3

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.035
DANN	Benign	0.34
PhyloP100		-2.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs7676; hg19: chr21-45565473;