rs10773980

Variant names:

• chr12-1689552-C-T
• rs10773980
• ENST00000537545.1:n.144+835C>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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000537545.1	n.144+835C>T		intron_variant	Intron 1 of 2	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;