rs2923084

Positions:

• chr11-10367235-A-G
• chr11-10367235-A-T

Variant summary

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

The NR_103765.1(CAND1.11):​n.501+36526A>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 0.291 in 152,134 control chromosomes in the GnomAD database, including 8,091 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 0.29 (8091 hom., cov: 32)
• Consequence: CAND1.11 NR_103765.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAND1.11	NR_103765.1	n.501+36526A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AMPD3	ENST00000295663.9	n.51-25047A>G		intron_variant, non_coding_transcript_variant		1
AMPD3	ENST00000527261.5	n.501+36526A>G		intron_variant, non_coding_transcript_variant		1
AMPD3	ENST00000532966.1	n.119+9844A>G		intron_variant, non_coding_transcript_variant		1
AMPD3	ENST00000532250.5	c.-6+36526A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44158 AN: 152016 Hom.: 8079 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.291 AC: 44207 AN: 152134 Hom.: 8091 Cov.: 32 AF XY: 0.290 AC XY: 21590 AN XY: 74376

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.285

Alfa AF: 0.207 Hom.: 8786

Bravo AF: 0.323

Asia WGS AF: 0.307 AC: 1069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2923084; hg19: chr11-10388782;