rs1539355

Variant names:

• chr1-202954952-A-G
• rs1539355
• NM_015999.6:c.-95+3233T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-202954952-A-G
• chr1-202954952-A-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.-95+3233T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 151,960 control chromosomes in the GnomAD database, including 8,615 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 0.33 (8615 hom., cov: 31)
• Consequence: ADIPOR1 NM_015999.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.664
• Publications: 11 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR1	NM_015999.6	c.-95+3233T>C		intron_variant	Intron 1 of 7	ENST00000340990.10	NP_057083.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR1	ENST00000340990.10	c.-95+3233T>C		intron_variant	Intron 1 of 7	1	NM_015999.6	ENSP00000341785.5
ADIPOR1	ENST00000367254.7	c.-95+3233T>C		intron_variant	Intron 1 of 6	1		ENSP00000356223.3
ADIPOR1	ENST00000417068.5	c.-161-645T>C		intron_variant	Intron 1 of 6	3		ENSP00000402178.1
ADIPOR1	ENST00000426229.1	c.-161-645T>C		intron_variant	Intron 1 of 5	2		ENSP00000392946.1

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49381 AN: 151842 Hom.: 8594 Cov.: 31

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.325 AC: 49439 AN: 151960 Hom.: 8615 Cov.: 31 AF XY: 0.317 AC XY: 23551 AN XY: 74270

African (AFR) AF: 0.452 AC: 18745 AN: 41426

American (AMR) AF: 0.240 AC: 3665 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 685 AN: 3464

East Asian (EAS) AF: 0.256 AC: 1327 AN: 5174

South Asian (SAS) AF: 0.167 AC: 798 AN: 4786

European-Finnish (FIN) AF: 0.237 AC: 2504 AN: 10564

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20801 AN: 67950

Other (OTH) AF: 0.333 AC: 704 AN: 2114

Alfa AF: 0.315 Hom.: 3156

Bravo AF: 0.334

Asia WGS AF: 0.231 AC: 799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.5
DANN	Benign	0.81
PhyloP100		0.66
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: rs1539355; hg19: chr1-202924080;