rs1539355

Positions:

• chr1-202954952-A-G
• chr1-202954952-A-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.81).
• 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/exons	MANE	UniProt
ADIPOR1	NM_015999.6	c.-95+3233T>C		intron_variant		ENST00000340990.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADIPOR1	ENST00000340990.10	c.-95+3233T>C		intron_variant		1	NM_015999.6	P1
ADIPOR1	ENST00000367254.7	c.-95+3233T>C		intron_variant		1
ADIPOR1	ENST00000417068.5	c.-161-645T>C		intron_variant		3
ADIPOR1	ENST00000426229.1	c.-161-645T>C		intron_variant		2

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

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.333

Alfa AF: 0.313 Hom.: 2554

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

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: rs1539355; hg19: chr1-202924080;