12-1780869-ATTTT-ATTT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_024551.3(ADIPOR2):​c.651-10delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000403 in 1,475,226 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: 𝑓 0.000053 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00044 ( 0 hom. )

Consequence

ADIPOR2
NM_024551.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0490
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAd4 at 8 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ADIPOR2NM_024551.3 linkc.651-10delT intron_variant Intron 5 of 7 ENST00000357103.5 NP_078827.2 Q86V24

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ADIPOR2ENST00000357103.5 linkc.651-19delT intron_variant Intron 5 of 7 1 NM_024551.3 ENSP00000349616.4 Q86V24
ADIPOR2ENST00000537190.1 linkn.491-19delT intron_variant Intron 1 of 1 2

Frequencies

GnomAD3 genomes
AF:
0.0000534
AC:
8
AN:
149834
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000491
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000664
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000743
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.000443
AC:
587
AN:
1325392
Hom.:
0
Cov.:
30
AF XY:
0.000510
AC XY:
335
AN XY:
656934
show subpopulations
Gnomad4 AFR exome
AF:
0.000348
Gnomad4 AMR exome
AF:
0.00144
Gnomad4 ASJ exome
AF:
0.000453
Gnomad4 EAS exome
AF:
0.000332
Gnomad4 SAS exome
AF:
0.000993
Gnomad4 FIN exome
AF:
0.000636
Gnomad4 NFE exome
AF:
0.000378
Gnomad4 OTH exome
AF:
0.000313
GnomAD4 genome
AF:
0.0000534
AC:
8
AN:
149834
Hom.:
0
Cov.:
32
AF XY:
0.0000411
AC XY:
3
AN XY:
73034
show subpopulations
Gnomad4 AFR
AF:
0.0000491
Gnomad4 AMR
AF:
0.0000664
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000743
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.00326
Hom.:
0
Bravo
AF:
0.0000604

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs745813254; hg19: chr12-1890035; API