dbSNP rs2275736: ADIPOR1:c.806-139T>A (chr1-202942357-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_015999.6(ADIPOR1):c.806-139T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0361 in 732,098 control chromosomes in the GnomAD database, including 2,070 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 0.076 ( 1116 hom., cov: 32)

Exomes 𝑓: 0.026 ( 954 hom. )

Consequence

ADIPOR1
NM_015999.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0280

Publications

2 publications found

Variant links:

Genes affected

ADIPOR1 (HGNC:24040): (adiponectin receptor 1) This gene encodes a protein which acts as a receptor for adiponectin, a hormone secreted by adipocytes which regulates fatty acid catabolism and glucose levels. Binding of adiponectin to the encoded protein results in activation of an AMP-activated kinase signaling pathway which affects levels of fatty acid oxidation and insulin sensitivity. A pseudogene of this gene is located on chromosome 14. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2014]

ADIPOR1 Gene-Disease associations (from GenCC):

retinitis pigmentosa
Inheritance: AD Classification: LIMITED Submitted by: Franklin by Genoox

ADIPOR1 links:

Genome browser will be placed here

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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR1	NM_015999.6 link	c.806-139T>A		intron_variant	Intron 6 of 7	ENST00000340990.10	NP_057083.2	Q96A54

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ADIPOR1	ENST00000340990.10 link	c.806-139T>A	intron_variant	Intron 6 of 7	1	NM_015999.6	ENSP00000341785.5	Q96A54
ADIPOR1	ENST00000367254.7 link	c.*21-139T>A	intron_variant	Intron 5 of 6	1		ENSP00000356223.3	F8W782
ADIPOR1	ENST00000495562.5 link	n.1040-139T>A	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.0760

AC:

11561

AN:

152206

Hom.:

1104

Cov.:

show subpopulations

Gnomad AFR

AF:

0.212

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0368

Gnomad ASJ

AF:

0.00346

Gnomad EAS

AF:

0.210

Gnomad SAS

AF:

0.0985

Gnomad FIN

AF:

0.00320

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.00660

Gnomad OTH

AF:

0.0607

GnomAD4 exome

AF:

0.0256

AC:

14851

AN:

579774

Hom.:

954

AF XY:

0.0269

AC XY:

7936

AN XY:

295350

show subpopulations

African (AFR)

AF:

0.206

AC:

3025

AN:

14650

American (AMR)

AF:

0.0318

AC:

506

AN:

15906

Ashkenazi Jewish (ASJ)

AF:

0.00338

AC:

AN:

14196

East Asian (EAS)

AF:

0.148

AC:

4469

AN:

30268

South Asian (SAS)

AF:

0.0800

AC:

3066

AN:

38316

European-Finnish (FIN)

AF:

0.00188

AC:

AN:

31334

Middle Eastern (MID)

AF:

0.0273

AC:

AN:

2270

European-Non Finnish (NFE)

AF:

0.00615

AC:

2479

AN:

402924

Other (OTH)

AF:

0.0380

AC:

1137

AN:

29910

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

642

1284

1926

2568

3210

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

174

348

522

696

870

<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:

0.0762

AC:

11603

AN:

152324

Hom.:

1116

Cov.:

AF XY:

0.0769

AC XY:

5729

AN XY:

74498

show subpopulations

African (AFR)

AF:

0.212

AC:

8825

AN:

41542

American (AMR)

AF:

0.0369

AC:

565

AN:

15312

Ashkenazi Jewish (ASJ)

AF:

0.00346

AC:

AN:

3472

East Asian (EAS)

AF:

0.210

AC:

1089

AN:

5190

South Asian (SAS)

AF:

0.0980

AC:

473

AN:

4828

European-Finnish (FIN)

AF:

0.00320

AC:

AN:

10628

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00661

AC:

450

AN:

68032

Other (OTH)

AF:

0.0676

AC:

143

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

478

957

1435

1914

2392

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

122

244

366

488

610

<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:

0.0472

Hom.:

Bravo

AF:

0.0848

Asia WGS

AF:

0.158

AC:

546

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.8

(source)

DANN

Benign

0.51

PhyloP100

0.028

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over