dbSNP rs10581: ADIPOR1:c.*383C>T (chr1-202941190-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_015999.6(ADIPOR1):c.*383C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.03 in 157,408 control chromosomes in the GnomAD database, including 130 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 0.030 ( 125 hom., cov: 32)

Exomes 𝑓: 0.033 ( 5 hom. )

Consequence

ADIPOR1
NM_015999.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.415

Publications

8 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=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR1	NM_015999.6 link	c.*383C>T		3_prime_UTR_variant	Exon 8 of 8	ENST00000340990.10	NP_057083.2	Q96A54

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR1	ENST00000340990.10 link	c.*383C>T		3_prime_UTR_variant	Exon 8 of 8	1	NM_015999.6	ENSP00000341785.5		Q96A54
ADIPOR1	ENST00000495562.5 link	n.1745C>T		non_coding_transcript_exon_variant	Exon 3 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.0300

AC:

4557

AN:

152132

Hom.:

126

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00864

Gnomad AMI

AF:

0.0165

Gnomad AMR

AF:

0.0176

Gnomad ASJ

AF:

0.0254

Gnomad EAS

AF:

0.113

Gnomad SAS

AF:

0.128

Gnomad FIN

AF:

0.0321

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0327

Gnomad OTH

AF:

0.0298

GnomAD4 exome

AF:

0.0328

AC:

169

AN:

5158

Hom.:

Cov.:

AF XY:

0.0351

AC XY:

AN XY:

2650

show subpopulations

African (AFR)

AF:

0.00746

AC:

AN:

134

American (AMR)

AF:

0.0103

AC:

AN:

292

Ashkenazi Jewish (ASJ)

AF:

0.0347

AC:

AN:

144

East Asian (EAS)

AF:

0.0921

AC:

AN:

228

South Asian (SAS)

AF:

0.115

AC:

AN:

208

European-Finnish (FIN)

AF:

0.0293

AC:

AN:

580

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0269

AC:

AN:

3276

Other (OTH)

AF:

0.0362

AC:

AN:

276

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome 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

GnomAD4 genome

AF:

0.0299

AC:

4554

AN:

152250

Hom.:

125

Cov.:

AF XY:

0.0312

AC XY:

2322

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.00864

AC:

359

AN:

41568

American (AMR)

AF:

0.0176

AC:

269

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0254

AC:

AN:

3468

East Asian (EAS)

AF:

0.112

AC:

580

AN:

5168

South Asian (SAS)

AF:

0.128

AC:

618

AN:

4820

European-Finnish (FIN)

AF:

0.0321

AC:

341

AN:

10610

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0327

AC:

2221

AN:

68012

Other (OTH)

AF:

0.0295

AC:

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

223

446

670

893

1116

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

140

210

280

350

<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:

0.0291

Hom.:

Bravo

AF:

0.0254

Asia WGS

AF:

0.115

AC:

401

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.61

(source)

DANN

Benign

0.70

PhyloP100

-0.41

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=99/1

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