rs17366653
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_004797.4(ADIPOQ):c.-8-24T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 1,613,402 control chromosomes in the GnomAD database, including 120 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 0.0085 ( 14 hom., cov: 33)
Exomes 𝑓: 0.010 ( 106 hom. )
Consequence
ADIPOQ
NM_004797.4 intron
NM_004797.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.93
Genes affected
ADIPOQ (HGNC:13633): (adiponectin, C1Q and collagen domain containing) This gene is expressed in adipose tissue exclusively. It encodes a protein with similarity to collagens X and VIII and complement factor C1q. The encoded protein circulates in the plasma and is involved with metabolic and hormonal processes. Mutations in this gene are associated with adiponectin deficiency. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Apr 2010]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BS2
?
High AC in GnomAd at 1298 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADIPOQ | NM_004797.4 | c.-8-24T>C | intron_variant | ENST00000320741.7 | |||
ADIPOQ-AS1 | NR_046662.2 | n.2431A>G | non_coding_transcript_exon_variant | 4/4 | |||
ADIPOQ | NM_001177800.2 | c.-8-24T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADIPOQ | ENST00000320741.7 | c.-8-24T>C | intron_variant | 1 | NM_004797.4 | P1 | |||
ADIPOQ | ENST00000444204.2 | c.-8-24T>C | intron_variant | 1 | P1 | ||||
ADIPOQ-AS1 | ENST00000422718.1 | n.2302A>G | non_coding_transcript_exon_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00853 AC: 1298AN: 152224Hom.: 14 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
1298
AN:
152224
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00940 AC: 2345AN: 249372Hom.: 25 AF XY: 0.00981 AC XY: 1324AN XY: 134904
GnomAD3 exomes
AF:
AC:
2345
AN:
249372
Hom.:
AF XY:
AC XY:
1324
AN XY:
134904
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0104 AC: 15222AN: 1461060Hom.: 106 Cov.: 30 AF XY: 0.0103 AC XY: 7509AN XY: 726882
GnomAD4 exome
AF:
AC:
15222
AN:
1461060
Hom.:
Cov.:
30
AF XY:
AC XY:
7509
AN XY:
726882
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00851 AC: 1296AN: 152342Hom.: 14 Cov.: 33 AF XY: 0.00804 AC XY: 599AN XY: 74494
GnomAD4 genome
?
AF:
AC:
1296
AN:
152342
Hom.:
Cov.:
33
AF XY:
AC XY:
599
AN XY:
74494
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
6
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: 24
Find out detailed SpliceAI scores and Pangolin per-transcript scores at