rs1539355

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015999.6(ADIPOR1):​c.-95+3233T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 151,960 control chromosomes in the GnomAD database, including 8,615 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 0.33 ( 8615 hom., cov: 31)

Consequence

ADIPOR1
NM_015999.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.664
Variant links:
Genes affected
ADIPOR1 (HGNC:24040): (adiponectin receptor 1) This gene encodes a protein which acts as a receptor for adiponectin, a hormone secreted by adipocytes which regulates fatty acid catabolism and glucose levels. Binding of adiponectin to the encoded protein results in activation of an AMP-activated kinase signaling pathway which affects levels of fatty acid oxidation and insulin sensitivity. A pseudogene of this gene is located on chromosome 14. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ADIPOR1NM_015999.6 linkuse as main transcriptc.-95+3233T>C intron_variant ENST00000340990.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ADIPOR1ENST00000340990.10 linkuse as main transcriptc.-95+3233T>C intron_variant 1 NM_015999.6 P1
ADIPOR1ENST00000367254.7 linkuse as main transcriptc.-95+3233T>C intron_variant 1
ADIPOR1ENST00000417068.5 linkuse as main transcriptc.-161-645T>C intron_variant 3
ADIPOR1ENST00000426229.1 linkuse as main transcriptc.-161-645T>C intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.325
AC:
49381
AN:
151842
Hom.:
8594
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.452
Gnomad AMI
AF:
0.133
Gnomad AMR
AF:
0.240
Gnomad ASJ
AF:
0.198
Gnomad EAS
AF:
0.257
Gnomad SAS
AF:
0.168
Gnomad FIN
AF:
0.237
Gnomad MID
AF:
0.307
Gnomad NFE
AF:
0.306
Gnomad OTH
AF:
0.329
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.325
AC:
49439
AN:
151960
Hom.:
8615
Cov.:
31
AF XY:
0.317
AC XY:
23551
AN XY:
74270
show subpopulations
Gnomad4 AFR
AF:
0.452
Gnomad4 AMR
AF:
0.240
Gnomad4 ASJ
AF:
0.198
Gnomad4 EAS
AF:
0.256
Gnomad4 SAS
AF:
0.167
Gnomad4 FIN
AF:
0.237
Gnomad4 NFE
AF:
0.306
Gnomad4 OTH
AF:
0.333
Alfa
AF:
0.313
Hom.:
2554
Bravo
AF:
0.334
Asia WGS
AF:
0.231
AC:
799
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
5.5
DANN
Benign
0.81

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

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

Other links and lift over

dbSNP: rs1539355; hg19: chr1-202924080; API