rs9300298

Variant names:

• chr12-1757038-T-A
• rs9300298
• NM_024551.3:c.171+2524T>A

Your query was ambiguous. Multiple possible variants found:

• chr12-1757038-T-A
• chr12-1757038-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024551.3(ADIPOR2):​c.171+2524T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 151,974 control chromosomes in the GnomAD database, including 23,869 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 0.55 (23869 hom., cov: 31)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479
• Publications: 10 publications found

Genes affected

ADIPOR2 (HGNC:24041): (adiponectin receptor 2) The adiponectin receptors, ADIPOR1 (MIM 607945) and ADIPOR2, serve as receptors for globular and full-length adiponectin (MIM 605441) and mediate increased AMPK (see MIM 602739) and PPAR-alpha (PPARA; MIM 170998) ligand activities, as well as fatty acid oxidation and glucose uptake by adiponectin (Yamauchi et al., 2003 [PubMed 12802337]).[supplied by OMIM, Mar 2008]

RPS4XP14 (HGNC:36737): (ribosomal protein S4X pseudogene 14)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.171+2524T>A		intron_variant	Intron 2 of 7	ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.171+2524T>A		intron_variant	Intron 2 of 7	1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000537545.1	n.401+2524T>A		intron_variant	Intron 2 of 2	3
RPS4XP14	ENST00000493072.1	n.*193A>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83916 AN: 151856 Hom.: 23828 Cov.: 31

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.553 AC: 84009 AN: 151974 Hom.: 23869 Cov.: 31 AF XY: 0.555 AC XY: 41224 AN XY: 74258

African (AFR) AF: 0.678 AC: 28081 AN: 41422

American (AMR) AF: 0.619 AC: 9459 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1821 AN: 3468

East Asian (EAS) AF: 0.598 AC: 3094 AN: 5176

South Asian (SAS) AF: 0.581 AC: 2803 AN: 4828

European-Finnish (FIN) AF: 0.481 AC: 5075 AN: 10540

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31914 AN: 67954

Other (OTH) AF: 0.587 AC: 1239 AN: 2110

Alfa AF: 0.510 Hom.: 2568

Bravo AF: 0.570

Asia WGS AF: 0.611 AC: 2120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.42
PhyloP100		-0.48
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: rs9300298; hg19: chr12-1866204;