rs7975375

Variant names:

• chr12-1722619-T-C
• rs7975375
• NM_024551.3:c.-87+31428T>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+31428T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,162 control chromosomes in the GnomAD database, including 1,906 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 (1906 hom., cov: 31)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 7 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=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024551.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	NM_024551.3	MANE Select	c.-87+31428T>C		intron	N/A	NP_078827.2
	ADIPOR2	NM_001375363.1		c.-87+31428T>C		intron	N/A	NP_001362292.1
	ADIPOR2	NM_001375364.1		c.-248-13460T>C		intron	N/A	NP_001362293.1	Q86V24

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	ENST00000357103.5	TSL:1 MANE Select	c.-87+31428T>C		intron	N/A	ENSP00000349616.4	Q86V24
	ADIPOR2	ENST00000878990.1		c.-87+31428T>C		intron	N/A	ENSP00000549049.1
	ADIPOR2	ENST00000878964.1		c.-87+31428T>C		intron	N/A	ENSP00000549023.1

Frequencies

GnomAD3 genomes AF: 0.151 AC: 23015 AN: 152044 Hom.: 1902 Cov.: 31

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.151 AC: 23046 AN: 152162 Hom.: 1906 Cov.: 31 AF XY: 0.150 AC XY: 11136 AN XY: 74400

African (AFR) AF: 0.215 AC: 8916 AN: 41490

American (AMR) AF: 0.101 AC: 1547 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 581 AN: 3468

East Asian (EAS) AF: 0.103 AC: 535 AN: 5190

South Asian (SAS) AF: 0.156 AC: 755 AN: 4828

European-Finnish (FIN) AF: 0.103 AC: 1086 AN: 10586

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9220 AN: 67990

Other (OTH) AF: 0.161 AC: 339 AN: 2108

Alfa AF: 0.155 Hom.: 262

Bravo AF: 0.152

Asia WGS AF: 0.148 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	15
DANN	Benign	0.93
PhyloP100		1.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs7975375; hg19: chr12-1831785;