rs762421

Variant names:

• chr21-44195678-G-A
• rs762421
• ENST00000646873.1:c.312-12235G>A

Variant summary

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

The ENST00000646873.1(GATD3):​c.312-12235G>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 0.0013 (22 hom., cov: 9)
  • Failed GnomAD Quality Control
• Consequence: GATD3 ENST00000646873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 73 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=-1.02).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GATD3	ENST00000646873.1	c.312-12235G>A		intron_variant	Intron 3 of 4			ENSP00000494853.1
GATD3	ENST00000644251.1	c.429-6372G>A		intron_variant	Intron 4 of 4			ENSP00000495305.1
GATD3	ENST00000645487.1	n.*202-1493G>A		intron_variant	Intron 3 of 3			ENSP00000494347.1

Frequencies

GnomAD3 genomes AF: 0.00130 AC: 98 AN: 75414 Hom.: 21 Cov.: 9

Gnomad AFR AF: 0.00303

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000579

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: 0.00153

Gnomad OTH AF: 0.00198

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: AS_VQSR AF: 0.00134 AC: 101 AN: 75440 Hom.: 22 Cov.: 9 AF XY: 0.00107 AC XY: 39 AN XY: 36562

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00335 AC: 31 AN: 9260

American (AMR) AF: 0.000578 AC: 6 AN: 10388

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2082

East Asian (EAS) AF: 0.00 AC: 0 AN: 3366

South Asian (SAS) AF: 0.00 AC: 0 AN: 2176

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5970

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 144

European-Non Finnish (NFE) AF: 0.00153 AC: 62 AN: 40404

Other (OTH) AF: 0.00198 AC: 2 AN: 1012

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.614 Hom.: 114072

Asia WGS AF: 0.643 AC: 2237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.15
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs762421; hg19: chr21-45615561;