Genetic Variant ADIPOR2:c.651-10delT (chr12-1780869-AT-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_024551.3(ADIPOR2):c.651-10delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000403 in 1,475,226 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000053 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00044 ( 0 hom. )

Consequence

ADIPOR2
NM_024551.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0490

Publications

0 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High AC in GnomAd4 at 8 AD gene.

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.651-10delT	intron	N/A	NP_078827.2
ADIPOR2	NM_001375363.1		c.651-10delT	intron	N/A	NP_001362292.1
ADIPOR2	NM_001375364.1		c.651-10delT	intron	N/A	NP_001362293.1	Q86V24

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADIPOR2	ENST00000357103.5	TSL:1 MANE Select	c.651-19delT	intron	N/A	ENSP00000349616.4	Q86V24
ADIPOR2	ENST00000878990.1		c.729-19delT	intron	N/A	ENSP00000549049.1
ADIPOR2	ENST00000878964.1		c.651-19delT	intron	N/A	ENSP00000549023.1

Frequencies

GnomAD3 genomes

AF:

0.0000534

AC:

AN:

149834

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000491

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000664

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000743

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00145

AC:

207

AN:

142944

AF XY:

0.00168

show subpopulations

Gnomad AFR exome

AF:

0.000440

Gnomad AMR exome

AF:

0.00217

Gnomad ASJ exome

AF:

0.00243

Gnomad EAS exome

AF:

0.000865

Gnomad FIN exome

AF:

0.000975

Gnomad NFE exome

AF:

0.00142

Gnomad OTH exome

AF:

0.00204

GnomAD4 exome

AF:

0.000443

AC:

587

AN:

1325392

Hom.:

Cov.:

AF XY:

0.000510

AC XY:

335

AN XY:

656934

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.000348

AC:

AN:

28724

American (AMR)

AF:

0.00144

AC:

AN:

31842

Ashkenazi Jewish (ASJ)

AF:

0.000453

AC:

AN:

22062

East Asian (EAS)

AF:

0.000332

AC:

AN:

36188

South Asian (SAS)

AF:

0.000993

AC:

AN:

71482

European-Finnish (FIN)

AF:

0.000636

AC:

AN:

48744

Middle Eastern (MID)

AF:

0.000383

AC:

AN:

5216

European-Non Finnish (NFE)

AF:

0.000378

AC:

388

AN:

1026778

Other (OTH)

AF:

0.000313

AC:

AN:

54356

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.311

Heterozygous variant carriers

142

213

284

355

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000534

AC:

AN:

149834

Hom.:

Cov.:

AF XY:

0.0000411

AC XY:

AN XY:

73034

show subpopulations

African (AFR)

AF:

0.0000491

AC:

AN:

40712

American (AMR)

AF:

0.0000664

AC:

AN:

15058

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3450

East Asian (EAS)

AF:

0.00

AC:

AN:

5134

South Asian (SAS)

AF:

0.00

AC:

AN:

4716

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10226

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.0000743

AC:

AN:

67276

Other (OTH)

AF:

0.00

AC:

AN:

2034

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.531

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00326

Hom.:

Bravo

AF:

0.0000604

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.049

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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.

12-1780869-ATTTT-ATTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over