chr11-10369145-C-T

Variant names:

• chr11-10369145-C-T
• rs7119983
• ENST00000295663.9:n.51-23137C>T

Variant summary

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

The ENST00000295663.9(AMPD3):​n.51-23137C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,108 control chromosomes in the GnomAD database, including 4,274 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 0.21 (4274 hom., cov: 32)
• Consequence: AMPD3 ENST00000295663.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAND1.11	NR_103765.1	n.501+38436C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AMPD3	ENST00000295663.9	n.51-23137C>T		intron_variant	Intron 1 of 2	1
AMPD3	ENST00000527261.5	n.501+38436C>T		intron_variant	Intron 2 of 2	1
AMPD3	ENST00000532966.1	n.119+11754C>T		intron_variant	Intron 1 of 1	1
AMPD3	ENST00000532250.5	c.-6+38436C>T		intron_variant	Intron 2 of 3	4		ENSP00000432707.1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31973 AN: 151990 Hom.: 4260 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.211 AC: 32028 AN: 152108 Hom.: 4274 Cov.: 32 AF XY: 0.213 AC XY: 15856 AN XY: 74370

African (AFR) AF: 0.369 AC: 15316 AN: 41460

American (AMR) AF: 0.148 AC: 2256 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3466

East Asian (EAS) AF: 0.303 AC: 1567 AN: 5164

South Asian (SAS) AF: 0.235 AC: 1134 AN: 4832

European-Finnish (FIN) AF: 0.163 AC: 1724 AN: 10596

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8919 AN: 67996

Other (OTH) AF: 0.201 AC: 424 AN: 2112

Alfa AF: 0.169 Hom.: 456

Bravo AF: 0.218

Asia WGS AF: 0.280 AC: 970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.9
DANN	Benign	0.74
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs7119983; hg19: chr11-10390692;