rs17366568
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004797.4(ADIPOQ):c.-8-387G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0912 in 219,184 control chromosomes in the GnomAD database, including 1,200 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 0.088 ( 819 hom., cov: 32)
Exomes 𝑓: 0.098 ( 381 hom. )
Consequence
ADIPOQ
NM_004797.4 intron
NM_004797.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.07
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADIPOQ | NM_004797.4 | c.-8-387G>A | intron_variant | ENST00000320741.7 | |||
ADIPOQ-AS1 | NR_046662.2 | n.2794C>T | non_coding_transcript_exon_variant | 4/4 | |||
ADIPOQ | NM_001177800.2 | c.-8-387G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADIPOQ | ENST00000320741.7 | c.-8-387G>A | intron_variant | 1 | NM_004797.4 | P1 | |||
ADIPOQ | ENST00000444204.2 | c.-8-387G>A | intron_variant | 1 | P1 | ||||
ADIPOQ-AS1 | ENST00000422718.1 | n.2665C>T | non_coding_transcript_exon_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0882 AC: 13427AN: 152158Hom.: 820 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
13427
AN:
152158
Hom.:
Cov.:
32
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:
GnomAD4 exome AF: 0.0979 AC: 6553AN: 66908Hom.: 381 Cov.: 0 AF XY: 0.100 AC XY: 3489AN XY: 34798
GnomAD4 exome
AF:
AC:
6553
AN:
66908
Hom.:
Cov.:
0
AF XY:
AC XY:
3489
AN XY:
34798
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: 0.0882 AC: 13427AN: 152276Hom.: 819 Cov.: 32 AF XY: 0.0903 AC XY: 6719AN XY: 74446
GnomAD4 genome
?
AF:
AC:
13427
AN:
152276
Hom.:
Cov.:
32
AF XY:
AC XY:
6719
AN XY:
74446
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:
249
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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at