12-1717390-C-T

Position:

• chr12-1717390-C-T

Variant summary

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

The NM_024551.3(ADIPOR2):​c.-87+26199C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0512 in 152,198 control chromosomes in the GnomAD database, including 272 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 0.051 (272 hom., cov: 32)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.-87+26199C>T		intron_variant		ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.-87+26199C>T		intron_variant		1	NM_024551.3	ENSP00000349616	P1
ADIPOR2	ENST00000537545.1	n.144+28673C>T		intron_variant, non_coding_transcript_variant		3
ADIPOR2	ENST00000540974.1	n.149-13335C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0513 AC: 7797 AN: 152080 Hom.: 272 Cov.: 32

Gnomad AFR AF: 0.0141

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0925

Gnomad FIN AF: 0.0234

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0743

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0512 AC: 7793 AN: 152198 Hom.: 272 Cov.: 32 AF XY: 0.0496 AC XY: 3691 AN XY: 74416

Gnomad4 AFR AF: 0.0141

Gnomad4 AMR AF: 0.0603

Gnomad4 ASJ AF: 0.0769

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0923

Gnomad4 FIN AF: 0.0234

Gnomad4 NFE AF: 0.0743

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0711 Hom.: 209

Bravo AF: 0.0519

Asia WGS AF: 0.0360 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.51
DANN	Benign	0.71

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: rs12826079; hg19: chr12-1826556;