Genetic Variant ADIPOR2:c.-87+4523T>G (chr12-1695714-T-G) – 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.-87+4523T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 151,514 control chromosomes in the GnomAD database, including 1,494 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 0.12 ( 1493 hom., cov: 31)

Exomes 𝑓: 0.13 ( 1 hom. )

Consequence

ADIPOR2
NM_024551.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.105

Publications

10 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:

ENSG00000271500 (HGNC:):

ENSG00000271500 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.269 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
ADIPOR2	NM_024551.3	MANE Select	c.-87+4523T>G	intron	N/A	NP_078827.2
ADIPOR2	NM_001375363.1		c.-87+4523T>G	intron	N/A	NP_001362292.1
ADIPOR2	NM_001375364.1		c.-249+4501T>G	intron	N/A	NP_001362293.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ADIPOR2	ENST00000357103.5	TSL:1 MANE Select	c.-87+4523T>G	intron	N/A	ENSP00000349616.4
ADIPOR2	ENST00000537545.1	TSL:3	n.144+6997T>G	intron	N/A
ADIPOR2	ENST00000540974.1	TSL:3	n.51+4501T>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.122

AC:

18530

AN:

151368

Hom.:

1492

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0373

Gnomad AMI

AF:

0.220

Gnomad AMR

AF:

0.201

Gnomad ASJ

AF:

0.147

Gnomad EAS

AF:

0.281

Gnomad SAS

AF:

0.185

Gnomad FIN

AF:

0.0879

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.142

Gnomad OTH

AF:

0.148

GnomAD4 exome

AF:

0.125

AC:

AN:

Hom.:

AF XY:

0.167

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0833

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.400

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.122

AC:

18544

AN:

151482

Hom.:

1493

Cov.:

AF XY:

0.124

AC XY:

9146

AN XY:

73968

show subpopulations

African (AFR)

AF:

0.0373

AC:

1545

AN:

41388

American (AMR)

AF:

0.201

AC:

3063

AN:

15202

Ashkenazi Jewish (ASJ)

AF:

0.147

AC:

508

AN:

3456

East Asian (EAS)

AF:

0.281

AC:

1442

AN:

5132

South Asian (SAS)

AF:

0.184

AC:

883

AN:

4800

European-Finnish (FIN)

AF:

0.0879

AC:

909

AN:

10336

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.142

AC:

9628

AN:

67858

Other (OTH)

AF:

0.149

AC:

314

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

801

1603

2404

3206

4007

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

212

424

636

848

1060

<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:

0.0937

Hom.:

213

Bravo

AF:

0.131

Asia WGS

AF:

0.207

AC:

716

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.4

(source)

DANN

Benign

0.32

PhyloP100

0.10

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

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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