rs7134070

Positions:

• chr12-1758235-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024551.3(ADIPOR2):​c.171+3721T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.053 in 152,332 control chromosomes in the GnomAD database, including 541 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 0.053 (541 hom., cov: 32)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADIPOR2	NM_024551.3	c.171+3721T>C		intron_variant		ENST00000357103.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.171+3721T>C		intron_variant		1	NM_024551.3	P1
ADIPOR2	ENST00000537545.1	n.401+3721T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0528 AC: 8040 AN: 152214 Hom.: 538 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0327

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.0795

Gnomad SAS AF: 0.0815

Gnomad FIN AF: 0.00282

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00489

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0530 AC: 8069 AN: 152332 Hom.: 541 Cov.: 32 AF XY: 0.0543 AC XY: 4043 AN XY: 74500

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.0327

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.0798

Gnomad4 SAS AF: 0.0813

Gnomad4 FIN AF: 0.00282

Gnomad4 NFE AF: 0.00490

Gnomad4 OTH AF: 0.0520

Alfa AF: 0.0336 Hom.: 51

Bravo AF: 0.0572

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	11
DANN	Benign	0.63

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: rs7134070; hg19: chr12-1867401;