chr11-10323889-A-G

Position:

• chr11-10323889-A-G

Variant summary

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

The NR_103765.1(CAND1.11):​n.362-6681A>G 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 0.101 in 152,312 control chromosomes in the GnomAD database, including 936 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 0.10 (936 hom., cov: 32)
• Consequence: CAND1.11 NR_103765.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.516

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAND1.11	NR_103765.1	n.362-6681A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AMPD3	ENST00000527261.5	n.362-6681A>G		intron_variant, non_coding_transcript_variant		1
AMPD3	ENST00000532250.5	c.-146+6121A>G		intron_variant		4		ENSP00000432707

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15362 AN: 152194 Hom.: 937 Cov.: 32

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0806

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0673

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0960

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

GnomAD4 genome AF: 0.101 AC: 15367 AN: 152312 Hom.: 936 Cov.: 32 AF XY: 0.105 AC XY: 7811 AN XY: 74460

Gnomad4 AFR AF: 0.0738

Gnomad4 AMR AF: 0.0805

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0669

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0950

Alfa AF: 0.0623 Hom.: 86

Bravo AF: 0.0892

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.0
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16907654; hg19: chr11-10345436;