chr12-1696421-C-G

Variant names:

• chr12-1696421-C-G
• rs10848554
• NM_024551.3:c.-87+5230C>G

Variant summary

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

The NM_001375363.1(ADIPOR2):​c.-87+5230C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 147,550 control chromosomes in the GnomAD database, including 49,691 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 0.82 (49666 hom., cov: 22)
  • Exomes 𝑓: 0.93 (25 hom.)
• Consequence: ADIPOR2 NM_001375363.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 3 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]

ENSG00000271500 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375363.1. 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+5230C>G		intron	N/A	NP_078827.2
	ADIPOR2	NM_001375363.1		c.-87+5230C>G		intron	N/A	NP_001362292.1
	ADIPOR2	NM_001375364.1		c.-249+5208C>G		intron	N/A	NP_001362293.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	ENST00000357103.5	TSL:1 MANE Select	c.-87+5230C>G		intron	N/A	ENSP00000349616.4
	ADIPOR2	ENST00000878990.1		c.-87+5230C>G		intron	N/A	ENSP00000549049.1
	ADIPOR2	ENST00000878964.1		c.-87+5230C>G		intron	N/A	ENSP00000549023.1

Frequencies

GnomAD3 genomes AF: 0.817 AC: 120370 AN: 147408 Hom.: 49643 Cov.: 22

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.807

GnomAD4 exome AF: 0.929 AC: 52 AN: 56 Hom.: 25 Cov.: 0 AF XY: 0.921 AC XY: 35 AN XY: 38

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.833 AC: 5 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.938 AC: 45 AN: 48

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.817 AC: 120431 AN: 147494 Hom.: 49666 Cov.: 22 AF XY: 0.820 AC XY: 58789 AN XY: 71680

African (AFR) AF: 0.678 AC: 26805 AN: 39532

American (AMR) AF: 0.889 AC: 13206 AN: 14852

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2841 AN: 3460

East Asian (EAS) AF: 0.898 AC: 4556 AN: 5072

South Asian (SAS) AF: 0.821 AC: 3797 AN: 4626

European-Finnish (FIN) AF: 0.901 AC: 8531 AN: 9466

Middle Eastern (MID) AF: 0.833 AC: 240 AN: 288

European-Non Finnish (NFE) AF: 0.861 AC: 57918 AN: 67242

Other (OTH) AF: 0.808 AC: 1654 AN: 2046

Alfa AF: 0.713 Hom.: 920

Bravo AF: 0.809

Asia WGS AF: 0.833 AC: 2877 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.27
PhyloP100		-1.9
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: rs10848554; hg19: chr12-1805587;