chr3-186853407-A-G

Position:

• chr3-186853407-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004797.4(ADIPOQ):​c.214+135A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,168,384 control chromosomes in the GnomAD database, including 9,516 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 0.10 (1108 hom., cov: 33)
  • Exomes 𝑓: 0.12 (8408 hom.)
• Consequence: ADIPOQ NM_004797.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.627

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]

ADIPOQ-AS1 (HGNC:40648): (ADIPOQ antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADIPOQ	NM_004797.4	c.214+135A>G		intron_variant		ENST00000320741.7
ADIPOQ-AS1	NR_046662.2	n.2216-165T>C		intron_variant, non_coding_transcript_variant
ADIPOQ	NM_001177800.2	c.214+135A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.214+135A>G		intron_variant		1	NM_004797.4	P1
ADIPOQ	ENST00000444204.2	c.214+135A>G		intron_variant		1		P1
ADIPOQ-AS1	ENST00000422718.1	n.2087-165T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15941 AN: 152218 Hom.: 1110 Cov.: 33

Gnomad AFR AF: 0.0469

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0434

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.159

GnomAD4 exome AF: 0.118 AC: 120397 AN: 1016048 Hom.: 8408 AF XY: 0.119 AC XY: 61309 AN XY: 513630

Gnomad4 AFR exome AF: 0.0426

Gnomad4 AMR exome AF: 0.180

Gnomad4 ASJ exome AF: 0.197

Gnomad4 EAS exome AF: 0.292

Gnomad4 SAS exome AF: 0.127

Gnomad4 FIN exome AF: 0.0446

Gnomad4 NFE exome AF: 0.111

Gnomad4 OTH exome AF: 0.135

GnomAD4 genome AF: 0.105 AC: 15944 AN: 152336 Hom.: 1108 Cov.: 33 AF XY: 0.107 AC XY: 7955 AN XY: 74496

Gnomad4 AFR AF: 0.0469

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0434

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.160

Alfa AF: 0.106 Hom.: 167

Bravo AF: 0.113

Asia WGS AF: 0.208 AC: 720 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	5.9
DANN	Benign	0.71

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

Other links and lift over

dbSNP: rs2241767; hg19: chr3-186571196;