chr1-202957385-C-T

Variant names:

• chr1-202957385-C-T
• rs7514221
• NM_015999.6:c.-95+800G>A

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+800G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 151,762 control chromosomes in the GnomAD database, including 26,020 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 0.58 (26020 hom., cov: 30)
• Consequence: ADIPOR1 NM_015999.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 16 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 = 0.808 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.-95+800G>A		intron	N/A	NP_057083.2
	ADIPOR1	NM_001290553.2		c.-95+524G>A		intron	N/A	NP_001277482.1
	ADIPOR1	NM_001290557.1		c.-162+800G>A		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.-95+800G>A		intron	N/A	ENSP00000341785.5
	ADIPOR1	ENST00000367254.7	TSL:1	c.-95+800G>A		intron	N/A	ENSP00000356223.3
	ADIPOR1	ENST00000417068.5	TSL:3	c.-162+1090G>A		intron	N/A	ENSP00000402178.1

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88383 AN: 151644 Hom.: 25971 Cov.: 30

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.583 AC: 88492 AN: 151762 Hom.: 26020 Cov.: 30 AF XY: 0.584 AC XY: 43271 AN XY: 74134

African (AFR) AF: 0.594 AC: 24572 AN: 41344

American (AMR) AF: 0.615 AC: 9371 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1642 AN: 3466

East Asian (EAS) AF: 0.829 AC: 4270 AN: 5152

South Asian (SAS) AF: 0.576 AC: 2767 AN: 4804

European-Finnish (FIN) AF: 0.528 AC: 5529 AN: 10480

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.569 AC: 38691 AN: 67960

Other (OTH) AF: 0.582 AC: 1226 AN: 2108

Alfa AF: 0.573 Hom.: 105226

Bravo AF: 0.590

Asia WGS AF: 0.707 AC: 2456 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	1.3
DANN	Benign	0.47
PhyloP100		-0.29
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: rs7514221; hg19: chr1-202926513;