12-1780869-A-AT

Position:

• chr12-1780869-A-AT

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6 BS2

The NM_024551.3(ADIPOR2):​c.651-10dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00227 in 1,447,884 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.00035 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0025 (0 hom.)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: 0.0490

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 Likely_benign. Variant got -5 ACMG points.

• BP6: Variant 12-1780869-A-AT is Benign according to our data. Variant chr12-1780869-A-AT is described in ClinVar as [Likely_benign]. Clinvar id is 3056279.Status of the report is no_assertion_criteria_provided, 0 stars.
• BS2: High AC in GnomAd4 at 53 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.651-10dup		intron_variant		ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.651-10dup		intron_variant		1	NM_024551.3	ENSP00000349616	P1
ADIPOR2	ENST00000537190.1	n.491-10dup		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.000347 AC: 52 AN: 149808 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000295

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000598

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000584

Gnomad SAS AF: 0.000424

Gnomad FIN AF: 0.0000978

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000357

Gnomad OTH AF: 0.000492

GnomAD4 exome AF: 0.00249 AC: 3235 AN: 1297966 Hom.: 0 Cov.: 30 AF XY: 0.00254 AC XY: 1637 AN XY: 643470

Gnomad4 AFR exome AF: 0.00316

Gnomad4 AMR exome AF: 0.00587

Gnomad4 ASJ exome AF: 0.00371

Gnomad4 EAS exome AF: 0.00275

Gnomad4 SAS exome AF: 0.00563

Gnomad4 FIN exome AF: 0.00278

Gnomad4 NFE exome AF: 0.00213

Gnomad4 OTH exome AF: 0.00199

GnomAD4 genome AF: 0.000354 AC: 53 AN: 149918 Hom.: 0 Cov.: 32 AF XY: 0.000369 AC XY: 27 AN XY: 73142

Gnomad4 AFR AF: 0.000318

Gnomad4 AMR AF: 0.000597

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000586

Gnomad4 SAS AF: 0.000424

Gnomad4 FIN AF: 0.0000978

Gnomad4 NFE AF: 0.000357

Gnomad4 OTH AF: 0.000487

Bravo AF: 0.000332

Asia WGS AF: 0.00433 AC: 15 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

ADIPOR2-related disorder Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Mar 21, 2023

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs745813254; hg19: chr12-1890035;