chr1-202956690-G-A

Variant names:

• chr1-202956690-G-A
• rs10920533
• NM_015999.6:c.-95+1495C>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+1495C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,088 control chromosomes in the GnomAD database, including 4,228 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 (4228 hom., cov: 32)
• Consequence: ADIPOR1 NM_015999.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547
• Publications: 10 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=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015999.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR1	NM_015999.6	MANE Select	c.-95+1495C>T		intron	N/A	NP_057083.2
	ADIPOR1	NM_001290553.2		c.-95+1219C>T		intron	N/A	NP_001277482.1	Q96A54
	ADIPOR1	NM_001290557.1		c.-162+1495C>T		intron	N/A	NP_001277486.1	Q96A54

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR1	ENST00000340990.10	TSL:1 MANE Select	c.-95+1495C>T		intron	N/A	ENSP00000341785.5	Q96A54
	ADIPOR1	ENST00000367254.7	TSL:1	c.-95+1495C>T		intron	N/A	ENSP00000356223.3	F8W782
	ADIPOR1	ENST00000855702.1		c.-95+1219C>T		intron	N/A	ENSP00000525761.1

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33637 AN: 151970 Hom.: 4229 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0476

Gnomad SAS AF: 0.0661

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.221 AC: 33635 AN: 152088 Hom.: 4228 Cov.: 32 AF XY: 0.213 AC XY: 15831 AN XY: 74344

African (AFR) AF: 0.142 AC: 5908 AN: 41488

American (AMR) AF: 0.194 AC: 2958 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 674 AN: 3470

East Asian (EAS) AF: 0.0471 AC: 244 AN: 5178

South Asian (SAS) AF: 0.0655 AC: 316 AN: 4822

European-Finnish (FIN) AF: 0.235 AC: 2482 AN: 10566

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

European-Non Finnish (NFE) AF: 0.299 AC: 20326 AN: 67966

Other (OTH) AF: 0.251 AC: 529 AN: 2108

Alfa AF: 0.258 Hom.: 643

Bravo AF: 0.217

Asia WGS AF: 0.0670 AC: 231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.34
DANN	Benign	0.81
PhyloP100		-0.55
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: rs10920533; hg19: chr1-202925818;