rs1342387

Positions:

• chr1-202945228-T-C

Variant summary

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

The NM_015999.6(ADIPOR1):​c.431-59A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 1,418,200 control chromosomes in the GnomAD database, including 210,210 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 0.53 (21299 hom., cov: 32)
  • Exomes 𝑓: 0.54 (188911 hom.)
• Consequence: ADIPOR1 NM_015999.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOR1	NM_015999.6	c.431-59A>G		intron_variant		ENST00000340990.10	NP_057083.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOR1	ENST00000340990.10	c.431-59A>G		intron_variant		1	NM_015999.6	ENSP00000341785	P1
ADIPOR1	ENST00000367254.7	c.430+1211A>G		intron_variant		1		ENSP00000356223
ADIPOR1	ENST00000417068.5	c.431-59A>G		intron_variant		3		ENSP00000402178
ADIPOR1	ENST00000426229.1	c.431-59A>G		intron_variant		2		ENSP00000392946

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80196 AN: 151976 Hom.: 21263 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.528

GnomAD4 exome AF: 0.545 AC: 689667 AN: 1266106 Hom.: 188911 AF XY: 0.544 AC XY: 337321 AN XY: 620224

Gnomad4 AFR exome AF: 0.516

Gnomad4 AMR exome AF: 0.467

Gnomad4 ASJ exome AF: 0.464

Gnomad4 EAS exome AF: 0.554

Gnomad4 SAS exome AF: 0.495

Gnomad4 FIN exome AF: 0.497

Gnomad4 NFE exome AF: 0.554

Gnomad4 OTH exome AF: 0.537

GnomAD4 genome AF: 0.528 AC: 80277 AN: 152094 Hom.: 21299 Cov.: 32 AF XY: 0.525 AC XY: 39056 AN XY: 74348

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.533

Alfa AF: 0.538 Hom.: 28948

Bravo AF: 0.526

Asia WGS AF: 0.578 AC: 2008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.52
DANN	Benign	0.66

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: rs1342387; hg19: chr1-202914356;