NM_024551.3:c.-87+16256T>C

Variant names:

• chr12-1707447-T-C
• rs11061937
• NM_024551.3:c.-87+16256T>C

Variant summary

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

The NM_024551.3(ADIPOR2):​c.-87+16256T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 151,390 control chromosomes in the GnomAD database, including 8,259 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 0.32 (8259 hom., cov: 30)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972
• Publications: 9 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.-87+16256T>C		intron_variant	Intron 1 of 7	ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.-87+16256T>C		intron_variant	Intron 1 of 7	1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000537545.1	n.144+18730T>C		intron_variant	Intron 1 of 2	3
ADIPOR2	ENST00000540974.1	n.148+4465T>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.317 AC: 47988 AN: 151274 Hom.: 8252 Cov.: 30

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.317 AC: 48019 AN: 151390 Hom.: 8259 Cov.: 30 AF XY: 0.324 AC XY: 23966 AN XY: 73932

African (AFR) AF: 0.214 AC: 8821 AN: 41280

American (AMR) AF: 0.479 AC: 7281 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1085 AN: 3468

East Asian (EAS) AF: 0.499 AC: 2578 AN: 5162

South Asian (SAS) AF: 0.399 AC: 1910 AN: 4790

European-Finnish (FIN) AF: 0.370 AC: 3828 AN: 10340

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.314 AC: 21328 AN: 67854

Other (OTH) AF: 0.356 AC: 750 AN: 2106

Alfa AF: 0.313 Hom.: 1923

Bravo AF: 0.325

Asia WGS AF: 0.448 AC: 1552 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.62
PhyloP100		-0.97
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: rs11061937; hg19: chr12-1816613;