Genetic Variant NM_024551.3:c.*1541G>A (chr12-1787613-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024551.3(ADIPOR2):c.*1541G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0449 in 152,242 control chromosomes in the GnomAD database, including 263 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 0.045 ( 263 hom., cov: 32)

Exomes 𝑓: 0.38 ( 0 hom. )

Consequence

ADIPOR2
NM_024551.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.354

Publications

5 publications found

Variant links:

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]

ADIPOR2 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADIPOR2	NM_024551.3	MANE Select	c.*1541G>A	3_prime_UTR	Exon 8 of 8	NP_078827.2
ADIPOR2	NM_001375363.1		c.*1541G>A	3_prime_UTR	Exon 9 of 9	NP_001362292.1
ADIPOR2	NM_001375364.1		c.*1541G>A	3_prime_UTR	Exon 9 of 9	NP_001362293.1	Q86V24

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADIPOR2	ENST00000357103.5	TSL:1 MANE Select	c.*1541G>A	3_prime_UTR	Exon 8 of 8	ENSP00000349616.4	Q86V24
ADIPOR2	ENST00000878990.1		c.*1541G>A	3_prime_UTR	Exon 10 of 10	ENSP00000549049.1
ADIPOR2	ENST00000878964.1		c.*1541G>A	3_prime_UTR	Exon 9 of 9	ENSP00000549023.1

Frequencies

GnomAD3 genomes

AF:

0.0448

AC:

6819

AN:

152116

Hom.:

263

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0453

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0343

Gnomad ASJ

AF:

0.00576

Gnomad EAS

AF:

0.188

Gnomad SAS

AF:

0.0496

Gnomad FIN

AF:

0.124

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0261

Gnomad OTH

AF:

0.0431

GnomAD4 exome

AF:

0.375

AC:

AN:

Hom.:

Cov.:

AF XY:

0.333

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.592

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0449

AC:

6834

AN:

152234

Hom.:

263

Cov.:

AF XY:

0.0490

AC XY:

3645

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.0455

AC:

1890

AN:

41554

American (AMR)

AF:

0.0343

AC:

525

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.00576

AC:

AN:

3470

East Asian (EAS)

AF:

0.188

AC:

974

AN:

5174

South Asian (SAS)

AF:

0.0492

AC:

237

AN:

4818

European-Finnish (FIN)

AF:

0.124

AC:

1314

AN:

10576

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0261

AC:

1775

AN:

68022

Other (OTH)

AF:

0.0450

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

318

635

953

1270

1588

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

168

252

336

420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0259

Hom.:

Bravo

AF:

0.0390

Asia WGS

AF:

0.119

AC:

412

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

3.5

(source)

DANN

Benign

0.77

PhyloP100

-0.35

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over