chr1-202940846-G-C

Variant names:

• chr1-202940846-G-C
• rs7539542
• NM_015999.6:c.*727C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 55 publications found

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]

ADIPOR1 Gene-Disease associations (from GenCC):

• retinitis pigmentosa

  Inheritance: AD Classification: LIMITED Submitted by: Franklin by Genoox

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015999.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR1	NM_015999.6	MANE Select	c.*727C>G		3_prime_UTR	Exon 8 of 8	NP_057083.2
	ADIPOR1	NM_001290553.2		c.*727C>G		3_prime_UTR	Exon 8 of 8	NP_001277482.1	Q96A54
	ADIPOR1	NM_001290557.1		c.*727C>G		3_prime_UTR	Exon 9 of 9	NP_001277486.1	Q96A54

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR1	ENST00000340990.10	TSL:1 MANE Select	c.*727C>G		3_prime_UTR	Exon 8 of 8	ENSP00000341785.5	Q96A54
	ADIPOR1	ENST00000855702.1		c.*727C>G		3_prime_UTR	Exon 8 of 8	ENSP00000525761.1
	ADIPOR1	ENST00000855703.1		c.*727C>G		3_prime_UTR	Exon 9 of 9	ENSP00000525762.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.697 AC: 297 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AF: 0.750 AC: 3 AN: 4

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

African (AFR) AF: 0.383 AC: 15870 AN: 41444

American (AMR) AF: 0.613 AC: 9362 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2271 AN: 3466

East Asian (EAS) AF: 0.372 AC: 1925 AN: 5174

South Asian (SAS) AF: 0.459 AC: 2213 AN: 4826

European-Finnish (FIN) AF: 0.673 AC: 7094 AN: 10538

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46814 AN: 67988

Other (OTH) AF: 0.616 AC: 1300 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	15
DANN	Benign	0.88
PhyloP100		1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7539542; hg19: chr1-202909974;