rs10773980

Positions:

• chr12-1689552-C-T

Variant summary

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

The ENST00000537545.1(ADIPOR2):​n.144+835C>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 0.394 in 151,970 control chromosomes in the GnomAD database, including 13,870 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 0.39 (13870 hom., cov: 32)
• Consequence: ADIPOR2 ENST00000537545.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220

Genes affected

ADIPOR2 (HGNC:24041): (adiponectin receptor 2) The adiponectin receptors, ADIPOR1 (MIM 607945) and ADIPOR2, serve as receptors for globular and full-length adiponectin (MIM 605441) and mediate increased AMPK (see MIM 602739) and PPAR-alpha (PPARA; MIM 170998) ligand activities, as well as fatty acid oxidation and glucose uptake by adiponectin (Yamauchi et al., 2003 [PubMed 12802337]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADIPOR2	ENST00000537545.1	n.144+835C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59931 AN: 151850 Hom.: 13868 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.394 AC: 59939 AN: 151970 Hom.: 13870 Cov.: 32 AF XY: 0.394 AC XY: 29231 AN XY: 74250

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.377

Alfa AF: 0.473 Hom.: 5068

Bravo AF: 0.371

Asia WGS AF: 0.377 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.48
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10773980; hg19: chr12-1798718;