dbSNP rs3737884: ADIPOR1:c.618-131G>A (chr1-202944076-C-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.618-131G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0369 in 783,698 control chromosomes in the GnomAD database, including 2,224 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 ( 1117 hom., cov: 33)

Exomes 𝑓: 0.027 ( 1107 hom. )

Consequence

ADIPOR1
NM_015999.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.405

Publications

5 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=-0.82).

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.618-131G>A		intron_variant	Intron 5 of 7	ENST00000340990.10	NP_057083.2	Q96A54

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ADIPOR1	ENST00000340990.10 link	c.618-131G>A	intron_variant	Intron 5 of 7	1	NM_015999.6	ENSP00000341785.5	Q96A54
ADIPOR1	ENST00000367254.7 link	c.431-213G>A	intron_variant	Intron 4 of 6	1		ENSP00000356223.3	F8W782
ADIPOR1	ENST00000495562.5 link	n.721G>A	non_coding_transcript_exon_variant	Exon 1 of 3	2
ADIPOR1	ENST00000417068.5 link	c.618-131G>A	intron_variant	Intron 6 of 6	3		ENSP00000402178.1	C9JNM5

Frequencies

GnomAD3 genomes

AF:

0.0759

AC:

11553

AN:

152140

Hom.:

1105

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:

0.211

Gnomad SAS

AF:

0.0982

Gnomad FIN

AF:

0.00320

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.00660

Gnomad OTH

AF:

0.0611

GnomAD4 exome

AF:

0.0275

AC:

17347

AN:

631440

Hom.:

1107

Cov.:

AF XY:

0.0295

AC XY:

9536

AN XY:

323578

show subpopulations

African (AFR)

AF:

0.212

AC:

3294

AN:

15536

American (AMR)

AF:

0.0324

AC:

655

AN:

20192

Ashkenazi Jewish (ASJ)

AF:

0.00345

AC:

AN:

14778

East Asian (EAS)

AF:

0.154

AC:

4921

AN:

31930

South Asian (SAS)

AF:

0.0870

AC:

4240

AN:

48748

European-Finnish (FIN)

AF:

0.00254

AC:

100

AN:

39368

Middle Eastern (MID)

AF:

0.0269

AC:

AN:

2308

European-Non Finnish (NFE)

AF:

0.00650

AC:

2774

AN:

426866

Other (OTH)

AF:

0.0394

AC:

1250

AN:

31714

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

709

1419

2128

2838

3547

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

210

420

630

840

1050

<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:

11595

AN:

152258

Hom.:

1117

Cov.:

AF XY:

0.0769

AC XY:

5725

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.212

AC:

8817

AN:

41528

American (AMR)

AF:

0.0369

AC:

565

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.00346

AC:

AN:

3470

East Asian (EAS)

AF:

0.211

AC:

1090

AN:

5172

South Asian (SAS)

AF:

0.0977

AC:

471

AN:

4822

European-Finnish (FIN)

AF:

0.00320

AC:

AN:

10620

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00662

AC:

450

AN:

68018

Other (OTH)

AF:

0.0681

AC:

144

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

491

982

1474

1965

2456

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

240

360

480

600

<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:

0.157

AC:

545

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.3

(source)

DANN

Benign

0.38

PhyloP100

-0.41

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