12-1761359-T-C

Variant names:

• chr12-1761359-T-C
• rs7967137
• NM_024551.3:c.171+6845T>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.171+6845T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,182 control chromosomes in the GnomAD database, including 2,251 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 0.15 (2251 hom., cov: 32)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.767
• Publications: 6 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.171+6845T>C		intron_variant	Intron 2 of 7	ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.171+6845T>C		intron_variant	Intron 2 of 7	1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000537545.1	n.401+6845T>C		intron_variant	Intron 2 of 2	3
ADIPOR2	ENST00000543456.1	n.252+379T>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23419 AN: 152064 Hom.: 2248 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0904

Gnomad ASJ AF: 0.0907

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.0754

Gnomad FIN AF: 0.0989

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.154 AC: 23433 AN: 152182 Hom.: 2251 Cov.: 32 AF XY: 0.150 AC XY: 11146 AN XY: 74404

African (AFR) AF: 0.266 AC: 11051 AN: 41478

American (AMR) AF: 0.0901 AC: 1378 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0907 AC: 315 AN: 3472

East Asian (EAS) AF: 0.0243 AC: 126 AN: 5188

South Asian (SAS) AF: 0.0758 AC: 366 AN: 4826

European-Finnish (FIN) AF: 0.0989 AC: 1048 AN: 10598

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8796 AN: 68014

Other (OTH) AF: 0.143 AC: 302 AN: 2112

Alfa AF: 0.144 Hom.: 248

Bravo AF: 0.158

Asia WGS AF: 0.0570 AC: 199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.8
DANN	Benign	0.83
PhyloP100		0.77
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: rs7967137; hg19: chr12-1870525;