rs10494839

Positions:

• chr1-202953066-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015999.6(ADIPOR1):​c.-94-1902A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,020 control chromosomes in the GnomAD database, including 4,241 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 0.22 (4241 hom., cov: 32)
• Consequence: ADIPOR1 NM_015999.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.80

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADIPOR1	NM_015999.6	c.-94-1902A>G		intron_variant		ENST00000340990.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADIPOR1	ENST00000340990.10	c.-94-1902A>G		intron_variant		1	NM_015999.6	P1
ADIPOR1	ENST00000367254.7	c.-94-1902A>G		intron_variant		1
ADIPOR1	ENST00000417068.5	c.-95+1175A>G		intron_variant		3
ADIPOR1	ENST00000426229.1	c.-95+1175A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33778 AN: 151904 Hom.: 4242 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0485

Gnomad SAS AF: 0.0673

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.222 AC: 33774 AN: 152020 Hom.: 4241 Cov.: 32 AF XY: 0.214 AC XY: 15884 AN XY: 74284

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.0481

Gnomad4 SAS AF: 0.0668

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.253

Alfa AF: 0.281 Hom.: 12118

Bravo AF: 0.219

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0070
DANN	Benign	0.28

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: rs10494839; hg19: chr1-202922194;