1-202945228-T-C

Variant names:

• chr1-202945228-T-C
• rs1342387
• NM_015999.6:c.431-59A>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.431-59A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 1,418,200 control chromosomes in the GnomAD database, including 210,210 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 0.53 (21299 hom., cov: 32)
  • Exomes 𝑓: 0.54 (188911 hom.)
• Consequence: ADIPOR1 NM_015999.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 71 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 (EAS) allele frequency at 95% confidence interval = 0.602 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.431-59A>G		intron	N/A	NP_057083.2
	ADIPOR1	NM_001290553.2		c.431-59A>G		intron	N/A	NP_001277482.1	Q96A54
	ADIPOR1	NM_001290557.1		c.431-59A>G		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.431-59A>G		intron	N/A	ENSP00000341785.5	Q96A54
	ADIPOR1	ENST00000367254.7	TSL:1	c.430+1211A>G		intron	N/A	ENSP00000356223.3	F8W782
	ADIPOR1	ENST00000855702.1		c.431-59A>G		intron	N/A	ENSP00000525761.1

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80196 AN: 151976 Hom.: 21263 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.528

GnomAD4 exome AF: 0.545 AC: 689667 AN: 1266106 Hom.: 188911 AF XY: 0.544 AC XY: 337321 AN XY: 620224

African (AFR) AF: 0.516 AC: 14589 AN: 28280

American (AMR) AF: 0.467 AC: 10146 AN: 21732

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 9136 AN: 19678

East Asian (EAS) AF: 0.554 AC: 19960 AN: 36060

South Asian (SAS) AF: 0.495 AC: 29390 AN: 59334

European-Finnish (FIN) AF: 0.497 AC: 22534 AN: 45368

Middle Eastern (MID) AF: 0.438 AC: 1526 AN: 3486

European-Non Finnish (NFE) AF: 0.554 AC: 554546 AN: 1000298

Other (OTH) AF: 0.537 AC: 27840 AN: 51870

GnomAD4 genome AF: 0.528 AC: 80277 AN: 152094 Hom.: 21299 Cov.: 32 AF XY: 0.525 AC XY: 39056 AN XY: 74348

African (AFR) AF: 0.522 AC: 21633 AN: 41480

American (AMR) AF: 0.484 AC: 7401 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1634 AN: 3466

East Asian (EAS) AF: 0.620 AC: 3207 AN: 5172

South Asian (SAS) AF: 0.519 AC: 2501 AN: 4822

European-Finnish (FIN) AF: 0.479 AC: 5062 AN: 10560

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.549 AC: 37299 AN: 67992

Other (OTH) AF: 0.533 AC: 1125 AN: 2110

Alfa AF: 0.537 Hom.: 36437

Bravo AF: 0.526

Asia WGS AF: 0.578 AC: 2008 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	0.52
DANN	Benign	0.66
PhyloP100		-1.7
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: rs1342387; hg19: chr1-202914356;