rs7134070

Variant names:

• chr12-1758235-T-C
• rs7134070
• NM_024551.3:c.171+3721T>C

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+3721T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.053 in 152,332 control chromosomes in the GnomAD database, including 541 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 0.053 (541 hom., cov: 32)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• Publications: 4 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=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.171+3721T>C		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+3721T>C		intron_variant	Intron 2 of 7	1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000537545.1	n.401+3721T>C		intron_variant	Intron 2 of 2	3
RPS4XP14	ENST00000493072.1	n.-224A>G		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.0528 AC: 8040 AN: 152214 Hom.: 538 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0327

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.0795

Gnomad SAS AF: 0.0815

Gnomad FIN AF: 0.00282

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00489

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0530 AC: 8069 AN: 152332 Hom.: 541 Cov.: 32 AF XY: 0.0543 AC XY: 4043 AN XY: 74500

African (AFR) AF: 0.148 AC: 6137 AN: 41572

American (AMR) AF: 0.0327 AC: 500 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 137 AN: 3470

East Asian (EAS) AF: 0.0798 AC: 414 AN: 5186

South Asian (SAS) AF: 0.0813 AC: 393 AN: 4832

European-Finnish (FIN) AF: 0.00282 AC: 30 AN: 10622

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00490 AC: 333 AN: 68026

Other (OTH) AF: 0.0520 AC: 110 AN: 2114

Alfa AF: 0.0373 Hom.: 58

Bravo AF: 0.0572

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	11
DANN	Benign	0.63
PhyloP100		0.42
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: rs7134070; hg19: chr12-1867401;