NM_015999.6:c.258+85C>G

Variant names:

• chr1-202948219-G-C
• rs34010966
• NM_015999.6:c.258+85C>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+85C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0449 in 1,101,718 control chromosomes in the GnomAD database, including 1,461 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 0.042 (176 hom., cov: 32)
  • Exomes 𝑓: 0.045 (1285 hom.)
• Consequence: ADIPOR1 NM_015999.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.105 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+85C>G		intron	N/A	NP_057083.2
	ADIPOR1	NM_001290553.2		c.258+85C>G		intron	N/A	NP_001277482.1
	ADIPOR1	NM_001290557.1		c.258+85C>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+85C>G		intron	N/A	ENSP00000341785.5
	ADIPOR1	ENST00000367254.7	TSL:1	c.258+85C>G		intron	N/A	ENSP00000356223.3
	ADIPOR1	ENST00000417068.5	TSL:3	c.258+85C>G		intron	N/A	ENSP00000402178.1

Frequencies

GnomAD3 genomes AF: 0.0417 AC: 6335 AN: 152080 Hom.: 172 Cov.: 32

Gnomad AFR AF: 0.0427

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0240

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0294

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0371

Gnomad OTH AF: 0.0425

GnomAD4 exome AF: 0.0454 AC: 43092 AN: 949520 Hom.: 1285 AF XY: 0.0475 AC XY: 22703 AN XY: 478374

African (AFR) AF: 0.0447 AC: 928 AN: 20742

American (AMR) AF: 0.0203 AC: 503 AN: 24822

Ashkenazi Jewish (ASJ) AF: 0.0408 AC: 675 AN: 16542

East Asian (EAS) AF: 0.116 AC: 3888 AN: 33440

South Asian (SAS) AF: 0.102 AC: 5913 AN: 58184

European-Finnish (FIN) AF: 0.0334 AC: 1570 AN: 47076

Middle Eastern (MID) AF: 0.0442 AC: 127 AN: 2872

European-Non Finnish (NFE) AF: 0.0391 AC: 27507 AN: 703946

Other (OTH) AF: 0.0473 AC: 1981 AN: 41896

GnomAD4 genome AF: 0.0417 AC: 6352 AN: 152198 Hom.: 176 Cov.: 32 AF XY: 0.0422 AC XY: 3137 AN XY: 74422

African (AFR) AF: 0.0431 AC: 1789 AN: 41506

American (AMR) AF: 0.0240 AC: 367 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0375 AC: 130 AN: 3470

East Asian (EAS) AF: 0.111 AC: 577 AN: 5184

South Asian (SAS) AF: 0.113 AC: 544 AN: 4818

European-Finnish (FIN) AF: 0.0294 AC: 311 AN: 10584

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0371 AC: 2523 AN: 68020

Other (OTH) AF: 0.0421 AC: 89 AN: 2114

Alfa AF: 0.0385 Hom.: 21

Bravo AF: 0.0394

Asia WGS AF: 0.113 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.12
DANN	Benign	0.44
PhyloP100		-0.69
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs34010966; hg19: chr1-202917347; COSMIC: COSV61852220; COSMIC: COSV61852220;