11-10310117-A-C

Position:

• chr11-10310117-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_103765.1(CAND1.11):​n.361+1444A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,950 control chromosomes in the GnomAD database, including 12,086 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 (12086 hom., cov: 32)
• Consequence: CAND1.11 NR_103765.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568

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]

CAND1.11 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAND1.11	NR_103765.1	n.361+1444A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AMPD3	ENST00000527261.5	n.361+1444A>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57605 AN: 151828 Hom.: 12082 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.379 AC: 57632 AN: 151950 Hom.: 12086 Cov.: 32 AF XY: 0.381 AC XY: 28295 AN XY: 74248

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.356

Alfa AF: 0.414 Hom.: 2293

Bravo AF: 0.363

Asia WGS AF: 0.242 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	13
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4444073; hg19: chr11-10331664;