1-202945425-C-T

Position:

• chr1-202945425-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015999.6(ADIPOR1):​c.431-256G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 152,088 control chromosomes in the GnomAD database, including 21,289 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 (21289 hom., cov: 33)
• Consequence: ADIPOR1 NM_015999.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADIPOR1	NM_015999.6	c.431-256G>A		intron_variant		ENST00000340990.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADIPOR1	ENST00000340990.10	c.431-256G>A		intron_variant		1	NM_015999.6	P1
ADIPOR1	ENST00000367254.7	c.430+1014G>A		intron_variant		1
ADIPOR1	ENST00000417068.5	c.431-256G>A		intron_variant		3
ADIPOR1	ENST00000426229.1	c.431-256G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80181 AN: 151974 Hom.: 21253 Cov.: 33

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.528 AC: 80261 AN: 152088 Hom.: 21289 Cov.: 33 AF XY: 0.525 AC XY: 39050 AN XY: 74336

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.534

Alfa AF: 0.533 Hom.: 2575

Bravo AF: 0.526

Asia WGS AF: 0.577 AC: 2005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.1
DANN	Benign	0.31

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

Publications

LitVar

Other links and lift over

dbSNP: rs1342386; hg19: chr1-202914553;