rs3737884

Positions:

• chr1-202944076-C-T

Variant summary

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

The ENST00000340990.10(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 ENST00000340990.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405

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=-0.82).
• 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/exons	MANE	Protein	UniProt
ADIPOR1	NM_015999.6	c.618-131G>A		intron_variant		ENST00000340990.10	NP_057083.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOR1	ENST00000340990.10	c.618-131G>A		intron_variant		1	NM_015999.6	ENSP00000341785	P1
ADIPOR1	ENST00000367254.7	c.431-213G>A		intron_variant		1		ENSP00000356223
ADIPOR1	ENST00000417068.5	c.618-131G>A		intron_variant		3		ENSP00000402178
ADIPOR1	ENST00000495562.5	n.721G>A		non_coding_transcript_exon_variant	1/3	2

Frequencies

GnomAD3 genomes AF: 0.0759 AC: 11553 AN: 152140 Hom.: 1105 Cov.: 33

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.: 9 AF XY: 0.0295 AC XY: 9536 AN XY: 323578

Gnomad4 AFR exome AF: 0.212

Gnomad4 AMR exome AF: 0.0324

Gnomad4 ASJ exome AF: 0.00345

Gnomad4 EAS exome AF: 0.154

Gnomad4 SAS exome AF: 0.0870

Gnomad4 FIN exome AF: 0.00254

Gnomad4 NFE exome AF: 0.00650

Gnomad4 OTH exome AF: 0.0394

GnomAD4 genome AF: 0.0762 AC: 11595 AN: 152258 Hom.: 1117 Cov.: 33 AF XY: 0.0769 AC XY: 5725 AN XY: 74452

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.0369

Gnomad4 ASJ AF: 0.00346

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.0977

Gnomad4 FIN AF: 0.00320

Gnomad4 NFE AF: 0.00662

Gnomad4 OTH AF: 0.0681

Alfa AF: 0.0472 Hom.: 65

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
DANN	Benign	0.38

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: rs3737884; hg19: chr1-202913204;