1-202947555-G-C

Variant names:

• chr1-202947555-G-C
• rs16850797
• NM_015999.6:c.258+749C>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.258+749C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0372 in 151,868 control chromosomes in the GnomAD database, including 336 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 0.037 (336 hom., cov: 31)
• Consequence: ADIPOR1 NM_015999.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.21 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR1	NM_015999.6	MANE Select	c.258+749C>G		intron	N/A	NP_057083.2
	ADIPOR1	NM_001290553.2		c.258+749C>G		intron	N/A	NP_001277482.1
	ADIPOR1	NM_001290557.1		c.258+749C>G		intron	N/A	NP_001277486.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR1	ENST00000340990.10	TSL:1 MANE Select	c.258+749C>G		intron	N/A	ENSP00000341785.5
	ADIPOR1	ENST00000367254.7	TSL:1	c.258+749C>G		intron	N/A	ENSP00000356223.3
	ADIPOR1	ENST00000417068.5	TSL:3	c.258+749C>G		intron	N/A	ENSP00000402178.1

Frequencies

GnomAD3 genomes AF: 0.0371 AC: 5632 AN: 151752 Hom.: 330 Cov.: 31

Gnomad AFR AF: 0.00671

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.0609

Gnomad FIN AF: 0.0496

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.0208

Gnomad OTH AF: 0.0403

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

GnomAD4 genome AF: 0.0372 AC: 5651 AN: 151868 Hom.: 336 Cov.: 31 AF XY: 0.0415 AC XY: 3082 AN XY: 74204

African (AFR) AF: 0.00669 AC: 277 AN: 41404

American (AMR) AF: 0.124 AC: 1887 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.00634 AC: 22 AN: 3468

East Asian (EAS) AF: 0.221 AC: 1142 AN: 5172

South Asian (SAS) AF: 0.0618 AC: 297 AN: 4804

European-Finnish (FIN) AF: 0.0496 AC: 522 AN: 10514

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.0208 AC: 1411 AN: 67980

Other (OTH) AF: 0.0398 AC: 84 AN: 2108

Alfa AF: 0.00843 Hom.: 1

Bravo AF: 0.0421

Asia WGS AF: 0.133 AC: 462 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.53
PhyloP100		0.58
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: rs16850797; hg19: chr1-202916683;