chr3-186842993-G-A

Position:

• chr3-186842993-G-A

Variant summary

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

The NM_004797.4(ADIPOQ):​c.-9+244G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 152,082 control chromosomes in the GnomAD database, including 11,284 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 0.38 (11284 hom., cov: 32)
• Consequence: ADIPOQ NM_004797.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.-9+244G>A		intron_variant		ENST00000320741.7	NP_004788.1
ADIPOQ	NM_001177800.2	c.-60+244G>A		intron_variant			NP_001171271.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.-9+244G>A		intron_variant		1	NM_004797.4	ENSP00000320709	P1
ADIPOQ	ENST00000444204.2	c.-60+244G>A		intron_variant		1		ENSP00000389814	P1

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57164 AN: 151964 Hom.: 11272 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.342

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.376 AC: 57220 AN: 152082 Hom.: 11284 Cov.: 32 AF XY: 0.386 AC XY: 28716 AN XY: 74314

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.343

Alfa AF: 0.349 Hom.: 9817

Bravo AF: 0.366

Asia WGS AF: 0.416 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.0
DANN	Benign	0.49

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: rs182052; hg19: chr3-186560782;