rs10773991

Variant names:

• chr12-1776140-C-T
• rs10773991
• NM_024551.3:c.292-1714C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024551.3(ADIPOR2):​c.292-1714C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 151,954 control chromosomes in the GnomAD database, including 14,626 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 0.42 (14626 hom., cov: 31)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.292-1714C>T		intron_variant	Intron 3 of 7	ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.292-1714C>T		intron_variant	Intron 3 of 7	1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000535774.1	n.249-1714C>T		intron_variant	Intron 1 of 2	4
ADIPOR2	ENST00000543456.1	n.373-1714C>T		intron_variant	Intron 2 of 2	3
ADIPOR2	ENST00000544470.1	n.40-1714C>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63465 AN: 151836 Hom.: 14625 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.418 AC: 63473 AN: 151954 Hom.: 14626 Cov.: 31 AF XY: 0.417 AC XY: 30938 AN XY: 74230

African (AFR) AF: 0.220 AC: 9112 AN: 41436

American (AMR) AF: 0.371 AC: 5664 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1648 AN: 3468

East Asian (EAS) AF: 0.400 AC: 2062 AN: 5156

South Asian (SAS) AF: 0.419 AC: 2020 AN: 4818

European-Finnish (FIN) AF: 0.520 AC: 5468 AN: 10516

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 35999 AN: 67960

Other (OTH) AF: 0.389 AC: 821 AN: 2112

Alfa AF: 0.464 Hom.: 2304

Bravo AF: 0.396

Asia WGS AF: 0.380 AC: 1328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.5
DANN	Benign	0.72
PhyloP100		0.065
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10773991; hg19: chr12-1885306;