rs745813254

Variant names:

• chr12-1780869-ATTTT-A
• rs745813254
• NM_024551.3:c.651-13_651-10delTTTT

Your query was ambiguous. Multiple possible variants found:

• chr12-1780869-ATTTT-A
• chr12-1780869-ATTTT-ATTT
• chr12-1780869-ATTTT-ATTTTT
• chr12-1780869-ATTTT-ATTTTTT
• chr12-1780869-ATTTT-ATTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_024551.3(ADIPOR2):​c.651-13_651-10delTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000151 in 1,328,502 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000015 (0 hom.)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.482
• Publications: 0 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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024551.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	NM_024551.3	MANE Select	c.651-13_651-10delTTTT		intron	N/A	NP_078827.2
	ADIPOR2	NM_001375363.1		c.651-13_651-10delTTTT		intron	N/A	NP_001362292.1
	ADIPOR2	NM_001375364.1		c.651-13_651-10delTTTT		intron	N/A	NP_001362293.1	Q86V24

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	ENST00000357103.5	TSL:1 MANE Select	c.651-19_651-16delTTTT		intron	N/A	ENSP00000349616.4	Q86V24
	ADIPOR2	ENST00000878990.1		c.729-19_729-16delTTTT		intron	N/A	ENSP00000549049.1
	ADIPOR2	ENST00000878964.1		c.651-19_651-16delTTTT		intron	N/A	ENSP00000549023.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000151 AC: 2 AN: 1328502 Hom.: 0 AF XY: 0.00000152 AC XY: 1 AN XY: 658562

African (AFR) AF: 0.00 AC: 0 AN: 28794

American (AMR) AF: 0.00 AC: 0 AN: 31968

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22126

East Asian (EAS) AF: 0.00 AC: 0 AN: 36266

South Asian (SAS) AF: 0.00 AC: 0 AN: 71868

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 48944

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5218

European-Non Finnish (NFE) AF: 0.00000194 AC: 2 AN: 1028820

Other (OTH) AF: 0.00 AC: 0 AN: 54498

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.48

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.42		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.42		Position offset: 20

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs745813254; hg19: chr12-1890035;