rs2275736

Positions:

• chr1-202942357-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ADIPOR1	NM_015999.6	c.806-139T>A		intron_variant		ENST00000340990.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADIPOR1	ENST00000340990.10	c.806-139T>A		intron_variant		1	NM_015999.6	P1
ADIPOR1	ENST00000367254.7	c.*21-139T>A		intron_variant		1
ADIPOR1	ENST00000495562.5	n.1040-139T>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0760 AC: 11561 AN: 152206 Hom.: 1104 Cov.: 32

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

Gnomad4 AFR exome AF: 0.206

Gnomad4 AMR exome AF: 0.0318

Gnomad4 ASJ exome AF: 0.00338

Gnomad4 EAS exome AF: 0.148

Gnomad4 SAS exome AF: 0.0800

Gnomad4 FIN exome AF: 0.00188

Gnomad4 NFE exome AF: 0.00615

Gnomad4 OTH exome AF: 0.0380

GnomAD4 genome AF: 0.0762 AC: 11603 AN: 152324 Hom.: 1116 Cov.: 32 AF XY: 0.0769 AC XY: 5729 AN XY: 74498

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.0369

Gnomad4 ASJ AF: 0.00346

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.0980

Gnomad4 FIN AF: 0.00320

Gnomad4 NFE AF: 0.00661

Gnomad4 OTH AF: 0.0676

Alfa AF: 0.0472 Hom.: 65

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
DANN	Benign	0.51

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

LitVar

Other links and lift over

dbSNP: rs2275736; hg19: chr1-202911485;