rs7539542

Positions:

• chr1-202940846-G-C

Variant summary

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

The NM_015999.6(ADIPOR1):​c.*727C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 152,456 control chromosomes in the GnomAD database, including 26,908 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 0.58 (26803 hom., cov: 32)
  • Exomes 𝑓: 0.70 (105 hom.)
• Consequence: ADIPOR1 NM_015999.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

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=-0.47).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADIPOR1	NM_015999.6	c.*727C>G		3_prime_UTR_variant	8/8	ENST00000340990.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADIPOR1	ENST00000340990.10	c.*727C>G		3_prime_UTR_variant	8/8	1	NM_015999.6	P1
ADIPOR1	ENST00000495562.5	n.2089C>G		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87533 AN: 151904 Hom.: 26797 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.616

GnomAD4 exome AF: 0.699 AC: 302 AN: 432 Hom.: 105 Cov.: 0 AF XY: 0.673 AC XY: 175 AN XY: 260

Gnomad4 FIN exome AF: 0.697

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.576 AC: 87567 AN: 152024 Hom.: 26803 Cov.: 32 AF XY: 0.573 AC XY: 42584 AN XY: 74300

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.616

Alfa AF: 0.633 Hom.: 3900

Bravo AF: 0.567

Asia WGS AF: 0.422 AC: 1467 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	15
DANN	Benign	0.88

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: rs7539542; hg19: chr1-202909974;