chr1-202954050-T-C

Variant names:

• chr1-202954050-T-C
• rs10753929
• NM_015999.6:c.-94-2886A>G

Variant summary

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

The NM_015999.6(ADIPOR1):​c.-94-2886A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 152,174 control chromosomes in the GnomAD database, including 55,210 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 0.85 (55210 hom., cov: 31)
• Consequence: ADIPOR1 NM_015999.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 15 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR1	NM_015999.6	c.-94-2886A>G		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.-94-2886A>G		intron_variant	Intron 1 of 7	1	NM_015999.6	ENSP00000341785.5
ADIPOR1	ENST00000367254.7	c.-94-2886A>G		intron_variant	Intron 1 of 6	1		ENSP00000356223.3
ADIPOR1	ENST00000417068.5	c.-95+191A>G		intron_variant	Intron 2 of 6	3		ENSP00000402178.1
ADIPOR1	ENST00000426229.1	c.-95+191A>G		intron_variant	Intron 2 of 5	2		ENSP00000392946.1

Frequencies

GnomAD3 genomes AF: 0.851 AC: 129401 AN: 152056 Hom.: 55165 Cov.: 31

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.851 AC: 129503 AN: 152174 Hom.: 55210 Cov.: 31 AF XY: 0.849 AC XY: 63139 AN XY: 74394

African (AFR) AF: 0.810 AC: 33626 AN: 41510

American (AMR) AF: 0.875 AC: 13385 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.925 AC: 3213 AN: 3472

East Asian (EAS) AF: 0.902 AC: 4663 AN: 5170

South Asian (SAS) AF: 0.847 AC: 4080 AN: 4818

European-Finnish (FIN) AF: 0.778 AC: 8235 AN: 10582

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.873 AC: 59357 AN: 68014

Other (OTH) AF: 0.874 AC: 1846 AN: 2112

Alfa AF: 0.868 Hom.: 181093

Bravo AF: 0.856

Asia WGS AF: 0.866 AC: 3012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.2
DANN	Benign	0.82
PhyloP100		-1.4
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: rs10753929; hg19: chr1-202923178;