rs2838513

Variant names:

• chr21-44175491-G-A
• rs2838513
• ENST00000411956.1:n.3G>A

Your query was ambiguous. Multiple possible variants found:

• chr21-44175491-G-A
• chr21-44175491-G-C

Variant summary

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

The ENST00000411956.1(ENSG00000237604):​n.3G>A variant causes a non coding transcript exon 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 0.0014 (1 hom., cov: 10)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000237604 ENST00000411956.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 4 publications found

Genes affected

ENSG00000237604 (HGNC:):

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=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377139	XR_001755082.3	n.569-339C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000237604	ENST00000411956.1	n.3G>A		non_coding_transcript_exon_variant	Exon 1 of 2	3
GATD3	ENST00000646873.1	c.312-32422G>A		intron_variant	Intron 3 of 4			ENSP00000494853.1
GATD3	ENST00000449622.6	c.490-18133G>A		intron_variant	Intron 5 of 5	2		ENSP00000400044.2

Frequencies

GnomAD3 genomes AF: 0.00139 AC: 106 AN: 76040 Hom.: 0 Cov.: 10

Gnomad AFR AF: 0.00308

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000583

Gnomad ASJ AF: 0.000585

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000117

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 0

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00144 AC: 110 AN: 76144 Hom.: 1 Cov.: 10 AF XY: 0.00148 AC XY: 55 AN XY: 37084

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

African (AFR) AF: 0.00320 AC: 102 AN: 31898

American (AMR) AF: 0.000583 AC: 4 AN: 6866

Ashkenazi Jewish (ASJ) AF: 0.000585 AC: 1 AN: 1708

East Asian (EAS) AF: 0.00 AC: 0 AN: 2196

South Asian (SAS) AF: 0.00 AC: 0 AN: 2684

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3780

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 160

European-Non Finnish (NFE) AF: 0.000117 AC: 3 AN: 25714

Other (OTH) AF: 0.00 AC: 0 AN: 1002

⚠️ 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: 0.230 Hom.: 1495

Asia WGS AF: 0.606 AC: 2111 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	0.68
DANN	Benign	0.58
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2838513; hg19: chr21-45595374;