rs7944706

Variant names:

• chr11-10309764-G-A
• rs7944706
• ENST00000527261.5:n.361+1091G>A

Variant summary

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

The ENST00000527261.5(AMPD3):​n.361+1091G>A variant causes a intron change. The variant allele was found at a frequency of 0.384 in 152,050 control chromosomes in the GnomAD database, including 11,713 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 0.38 (11713 hom., cov: 33)
• Consequence: AMPD3 ENST00000527261.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.06
• Publications: 17 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=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAND1.11	NR_103765.1	n.361+1091G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AMPD3	ENST00000527261.5	n.361+1091G>A		intron_variant	Intron 1 of 2	1

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58376 AN: 151930 Hom.: 11715 Cov.: 33

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.384 AC: 58376 AN: 152050 Hom.: 11713 Cov.: 33 AF XY: 0.385 AC XY: 28582 AN XY: 74318

African (AFR) AF: 0.263 AC: 10923 AN: 41474

American (AMR) AF: 0.346 AC: 5281 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1644 AN: 3470

East Asian (EAS) AF: 0.447 AC: 2311 AN: 5170

South Asian (SAS) AF: 0.429 AC: 2071 AN: 4824

European-Finnish (FIN) AF: 0.436 AC: 4599 AN: 10546

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30013 AN: 67978

Other (OTH) AF: 0.421 AC: 888 AN: 2110

Alfa AF: 0.421 Hom.: 24734

Bravo AF: 0.370

Asia WGS AF: 0.453 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	20
DANN	Benign	0.69
PhyloP100		4.1

Splicing

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

Other links and lift over

dbSNP: rs7944706; hg19: chr11-10331311;