rs16850799

Variant names:

• chr1-202950723-G-A
• rs16850799
• NM_015999.6:c.141+207C>T

Variant summary

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

The NM_015999.6(ADIPOR1):​c.141+207C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,124 control chromosomes in the GnomAD database, including 4,167 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 0.21 (4167 hom., cov: 31)
• Consequence: ADIPOR1 NM_015999.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 18 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR1	NM_015999.6	MANE Select	c.141+207C>T		intron	N/A	NP_057083.2
	ADIPOR1	NM_001290553.2		c.141+207C>T		intron	N/A	NP_001277482.1
	ADIPOR1	NM_001290557.1		c.141+207C>T		intron	N/A	NP_001277486.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR1	ENST00000340990.10	TSL:1 MANE Select	c.141+207C>T		intron	N/A	ENSP00000341785.5
	ADIPOR1	ENST00000367254.7	TSL:1	c.141+207C>T		intron	N/A	ENSP00000356223.3
	ADIPOR1	ENST00000417068.5	TSL:3	c.141+207C>T		intron	N/A	ENSP00000402178.1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31882 AN: 152006 Hom.: 4155 Cov.: 31

Gnomad AFR AF: 0.0797

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.199

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.210 AC: 31916 AN: 152124 Hom.: 4167 Cov.: 31 AF XY: 0.218 AC XY: 16233 AN XY: 74342

African (AFR) AF: 0.0797 AC: 3309 AN: 41544

American (AMR) AF: 0.347 AC: 5293 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 817 AN: 3468

East Asian (EAS) AF: 0.460 AC: 2370 AN: 5148

South Asian (SAS) AF: 0.297 AC: 1434 AN: 4826

European-Finnish (FIN) AF: 0.260 AC: 2748 AN: 10568

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15330 AN: 67980

Other (OTH) AF: 0.200 AC: 423 AN: 2112

Alfa AF: 0.221 Hom.: 13877

Bravo AF: 0.210

Asia WGS AF: 0.362 AC: 1260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.98
DANN	Benign	0.43
PhyloP100		0.075
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: rs16850799; hg19: chr1-202919851; COSMIC: COSV61852756;