11-10382030-A-G

Variant names:

• chr11-10382030-A-G
• rs2198009
• ENST00000295663.9:n.51-10252A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000532250.5(AMPD3):​c.-6+51321A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 152,088 control chromosomes in the GnomAD database, including 17,085 homozygotes. 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 0.46 (17085 hom., cov: 33)
• Consequence: AMPD3 ENST00000532250.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.21
• Publications: 3 publications found

Genes affected

AMPD3 (HGNC:470): (adenosine monophosphate deaminase 3) This gene encodes a member of the AMP deaminase gene family. The encoded protein is a highly regulated enzyme that catalyzes the hydrolytic deamination of adenosine monophosphate to inosine monophosphate, a branch point in the adenylate catabolic pathway. This gene encodes the erythrocyte (E) isoforms, whereas other family members encode isoforms that predominate in muscle (M) and liver (L) cells. Mutations in this gene lead to the clinically asymptomatic, autosomal recessive condition erythrocyte AMP deaminase deficiency. Alternatively spliced transcript variants encoding different isoforms of this gene have been described. [provided by RefSeq, Jul 2008]

AMPD3 Gene-Disease associations (from GenCC):

• adenosine monophosphate deaminase deficiency

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

CAND1.11 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000532250.5. 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
	CAND1.11	NR_103765.1		n.502-28727A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AMPD3	ENST00000295663.9	TSL:1	n.51-10252A>G		intron	N/A
	AMPD3	ENST00000527261.5	TSL:1	n.502-28727A>G		intron	N/A
	AMPD3	ENST00000532966.1	TSL:1	n.119+24639A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70095 AN: 151970 Hom.: 17086 Cov.: 33

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.494

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.461 AC: 70098 AN: 152088 Hom.: 17085 Cov.: 33 AF XY: 0.464 AC XY: 34509 AN XY: 74324

African (AFR) AF: 0.291 AC: 12076 AN: 41480

American (AMR) AF: 0.584 AC: 8932 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1965 AN: 3468

East Asian (EAS) AF: 0.531 AC: 2751 AN: 5180

South Asian (SAS) AF: 0.413 AC: 1992 AN: 4828

European-Finnish (FIN) AF: 0.539 AC: 5696 AN: 10560

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.515 AC: 35022 AN: 67970

Other (OTH) AF: 0.491 AC: 1038 AN: 2112

Alfa AF: 0.494 Hom.: 9361

Bravo AF: 0.457

Asia WGS AF: 0.480 AC: 1672 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	13
DANN	Benign	0.79
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs2198009; hg19: chr11-10403577;