rs7514296

Positions:

• chr1-202957430-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.-95+755G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0801 in 151,878 control chromosomes in the GnomAD database, including 1,219 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 0.080 (1219 hom., cov: 32)
• Consequence: ADIPOR1 NM_015999.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

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=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADIPOR1	NM_015999.6	c.-95+755G>A		intron_variant		ENST00000340990.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADIPOR1	ENST00000340990.10	c.-95+755G>A		intron_variant		1	NM_015999.6	P1
ADIPOR1	ENST00000367254.7	c.-95+755G>A		intron_variant		1
ADIPOR1	ENST00000417068.5	c.-162+1045G>A		intron_variant		3
ADIPOR1	ENST00000426229.1	c.-162+755G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0798 AC: 12117 AN: 151758 Hom.: 1205 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0361

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.0997

Gnomad FIN AF: 0.00322

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.00722

Gnomad OTH AF: 0.0651

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

GnomAD4 genome AF: 0.0801 AC: 12165 AN: 151878 Hom.: 1219 Cov.: 32 AF XY: 0.0809 AC XY: 6004 AN XY: 74226

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.0362

Gnomad4 ASJ AF: 0.00346

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.0991

Gnomad4 FIN AF: 0.00322

Gnomad4 NFE AF: 0.00723

Gnomad4 OTH AF: 0.0720

Alfa AF: 0.0514 Hom.: 98

Bravo AF: 0.0885

Asia WGS AF: 0.155 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	11
DANN	Benign	0.84

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: rs7514296; hg19: chr1-202926558;