rs3737884

Variant names:

• chr1-202944076-C-T
• rs3737884
• NM_015999.6:c.618-131G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015999.6(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 NM_015999.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405
• Publications: 5 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 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.618-131G>A		intron	N/A	NP_057083.2
	ADIPOR1	NM_001290553.2		c.618-131G>A		intron	N/A	NP_001277482.1	Q96A54
	ADIPOR1	NM_001290557.1		c.618-131G>A		intron	N/A	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.618-131G>A		intron	N/A	ENSP00000341785.5	Q96A54
	ADIPOR1	ENST00000367254.7	TSL:1	c.431-213G>A		intron	N/A	ENSP00000356223.3	F8W782
	ADIPOR1	ENST00000855702.1		c.618-131G>A		intron	N/A	ENSP00000525761.1

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

African (AFR) AF: 0.212 AC: 3294 AN: 15536

American (AMR) AF: 0.0324 AC: 655 AN: 20192

Ashkenazi Jewish (ASJ) AF: 0.00345 AC: 51 AN: 14778

East Asian (EAS) AF: 0.154 AC: 4921 AN: 31930

South Asian (SAS) AF: 0.0870 AC: 4240 AN: 48748

European-Finnish (FIN) AF: 0.00254 AC: 100 AN: 39368

Middle Eastern (MID) AF: 0.0269 AC: 62 AN: 2308

European-Non Finnish (NFE) AF: 0.00650 AC: 2774 AN: 426866

Other (OTH) AF: 0.0394 AC: 1250 AN: 31714

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

African (AFR) AF: 0.212 AC: 8817 AN: 41528

American (AMR) AF: 0.0369 AC: 565 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00346 AC: 12 AN: 3470

East Asian (EAS) AF: 0.211 AC: 1090 AN: 5172

South Asian (SAS) AF: 0.0977 AC: 471 AN: 4822

European-Finnish (FIN) AF: 0.00320 AC: 34 AN: 10620

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00662 AC: 450 AN: 68018

Other (OTH) AF: 0.0681 AC: 144 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.38
PhyloP100		-0.41
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3737884;

hg19: chr1-202913204;