11-10369145-C-T

Position:

• chr11-10369145-C-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+38436C>T 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 0.211 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: CAND1.11 NR_103765.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

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=-0.95).
• 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/exons	MANE	Protein	UniProt
CAND1.11	NR_103765.1	n.501+38436C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AMPD3	ENST00000295663.9	n.51-23137C>T		intron_variant, non_coding_transcript_variant		1
AMPD3	ENST00000527261.5	n.501+38436C>T		intron_variant, non_coding_transcript_variant		1
AMPD3	ENST00000532966.1	n.119+11754C>T		intron_variant, non_coding_transcript_variant		1
AMPD3	ENST00000532250.5	c.-6+38436C>T		intron_variant		4		ENSP00000432707

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

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.201

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7119983; hg19: chr11-10390692;