rs3774262

Variant names:

• chr3-186854025-G-A
• rs3774262
• NM_004797.4:c.215-159G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-186854025-G-A
• chr3-186854025-G-C

Variant summary

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

The NM_004797.4(ADIPOQ):​c.215-159G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 687,612 control chromosomes in the GnomAD database, including 6,065 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 (1105 hom., cov: 31)
  • Exomes 𝑓: 0.12 (4960 hom.)
• Consequence: ADIPOQ NM_004797.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335

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=-0.85).
• 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 rank	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.215-159G>A		intron_variant	Intron 2 of 2	ENST00000320741.7	NP_004788.1
ADIPOQ	NM_001177800.2	c.215-159G>A		intron_variant	Intron 3 of 3		NP_001171271.1
ADIPOQ-AS1	NR_046662.2	n.2120+108C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.215-159G>A		intron_variant	Intron 2 of 2	1	NM_004797.4	ENSP00000320709.2
ADIPOQ	ENST00000444204.2	c.215-159G>A		intron_variant	Intron 3 of 3	1		ENSP00000389814.2
ADIPOQ-AS1	ENST00000422718.1	n.1991+108C>T		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15886 AN: 151938 Hom.: 1106 Cov.: 31

Gnomad AFR AF: 0.0468

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0432

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.159

GnomAD4 exome AF: 0.122 AC: 65116 AN: 535556 Hom.: 4960 Cov.: 7 AF XY: 0.122 AC XY: 33926 AN XY: 277254

Gnomad4 AFR exome AF: 0.0428

Gnomad4 AMR exome AF: 0.176

Gnomad4 ASJ exome AF: 0.200

Gnomad4 EAS exome AF: 0.293

Gnomad4 SAS exome AF: 0.126

Gnomad4 FIN exome AF: 0.0445

Gnomad4 NFE exome AF: 0.109

Gnomad4 OTH exome AF: 0.135

GnomAD4 genome AF: 0.105 AC: 15896 AN: 152056 Hom.: 1105 Cov.: 31 AF XY: 0.107 AC XY: 7930 AN XY: 74332

Gnomad4 AFR AF: 0.0469

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0432

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.163

Alfa AF: 0.122 Hom.: 2090

Bravo AF: 0.113

Asia WGS AF: 0.207 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.6
DANN	Benign	0.34

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: rs3774262; hg19: chr3-186571814; COSMIC: COSV57860255;