chr12-1707976-C-T

Variant names:

• chr12-1707976-C-T
• rs11832817
• NM_024551.3:c.-87+16785C>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.-87+16785C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 151,918 control chromosomes in the GnomAD database, including 6,259 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 0.27 (6259 hom., cov: 32)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 4 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.-87+16785C>T		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+16785C>T		intron_variant	Intron 1 of 7	1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000537545.1	n.144+19259C>T		intron_variant	Intron 1 of 2	3
ADIPOR2	ENST00000540974.1	n.148+4994C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41342 AN: 151800 Hom.: 6258 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.272 AC: 41354 AN: 151918 Hom.: 6259 Cov.: 32 AF XY: 0.275 AC XY: 20438 AN XY: 74242

African (AFR) AF: 0.167 AC: 6905 AN: 41426

American (AMR) AF: 0.443 AC: 6762 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1066 AN: 3472

East Asian (EAS) AF: 0.321 AC: 1659 AN: 5164

South Asian (SAS) AF: 0.345 AC: 1663 AN: 4818

European-Finnish (FIN) AF: 0.248 AC: 2609 AN: 10526

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19604 AN: 67952

Other (OTH) AF: 0.310 AC: 652 AN: 2106

Alfa AF: 0.263 Hom.: 774

Bravo AF: 0.285

Asia WGS AF: 0.313 AC: 1086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.8
DANN	Benign	0.67
PhyloP100		-1.4
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: rs11832817; hg19: chr12-1817142;