rs10581

Positions:

• chr1-202941190-G-A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

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=-0.83).
• 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/exons	MANE	Protein	UniProt
ADIPOR1	NM_015999.6	c.*383C>T		3_prime_UTR_variant	8/8	ENST00000340990.10	NP_057083.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOR1	ENST00000340990.10	c.*383C>T		3_prime_UTR_variant	8/8	1	NM_015999.6	ENSP00000341785	P1
ADIPOR1	ENST00000495562.5	n.1745C>T		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.0300 AC: 4557 AN: 152132 Hom.: 126 Cov.: 32

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.: 5 Cov.: 0 AF XY: 0.0351 AC XY: 93 AN XY: 2650

Gnomad4 AFR exome AF: 0.00746

Gnomad4 AMR exome AF: 0.0103

Gnomad4 ASJ exome AF: 0.0347

Gnomad4 EAS exome AF: 0.0921

Gnomad4 SAS exome AF: 0.115

Gnomad4 FIN exome AF: 0.0293

Gnomad4 NFE exome AF: 0.0269

Gnomad4 OTH exome AF: 0.0362

GnomAD4 genome AF: 0.0299 AC: 4554 AN: 152250 Hom.: 125 Cov.: 32 AF XY: 0.0312 AC XY: 2322 AN XY: 74444

Gnomad4 AFR AF: 0.00864

Gnomad4 AMR AF: 0.0176

Gnomad4 ASJ AF: 0.0254

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.0321

Gnomad4 NFE AF: 0.0327

Gnomad4 OTH AF: 0.0295

Alfa AF: 0.0301 Hom.: 53

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
DANN	Benign	0.70
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs10581; hg19: chr1-202910318;