rs10920534

Variant names:

• chr1-202957941-C-T
• rs10920534
• NM_015999.6:c.-95+244G>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.-95+244G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,152 control chromosomes in the GnomAD database, including 3,947 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 0.20 (3947 hom., cov: 33)
• Consequence: ADIPOR1 NM_015999.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571
• Publications: 9 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=-0.72).
• 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 rank	MANE	Protein	UniProt
ADIPOR1	NM_015999.6	c.-95+244G>A		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+244G>A		intron_variant	Intron 1 of 7	1	NM_015999.6	ENSP00000341785.5
ADIPOR1	ENST00000367254.7	c.-95+244G>A		intron_variant	Intron 1 of 6	1		ENSP00000356223.3
ADIPOR1	ENST00000417068.5	c.-162+534G>A		intron_variant	Intron 1 of 6	3		ENSP00000402178.1
ADIPOR1	ENST00000426229.1	c.-162+244G>A		intron_variant	Intron 1 of 5	2		ENSP00000392946.1

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31100 AN: 152034 Hom.: 3949 Cov.: 33

Gnomad AFR AF: 0.0842

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0467

Gnomad SAS AF: 0.0671

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.204 AC: 31089 AN: 152152 Hom.: 3947 Cov.: 33 AF XY: 0.197 AC XY: 14661 AN XY: 74402

African (AFR) AF: 0.0840 AC: 3490 AN: 41536

American (AMR) AF: 0.188 AC: 2872 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 667 AN: 3472

East Asian (EAS) AF: 0.0462 AC: 238 AN: 5150

South Asian (SAS) AF: 0.0665 AC: 321 AN: 4824

European-Finnish (FIN) AF: 0.234 AC: 2485 AN: 10616

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20307 AN: 67926

Other (OTH) AF: 0.242 AC: 511 AN: 2114

Alfa AF: 0.247 Hom.: 619

Bravo AF: 0.197

Asia WGS AF: 0.0650 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	6.9
DANN	Benign	0.69
PhyloP100		-0.57
PromoterAI		-0.16	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10920534; hg19: chr1-202927069;