chr3-186853334-G-T

Variant names:

• chr3-186853334-G-T
• rs1501299
• NM_004797.4:c.214+62G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004797.4(ADIPOQ):​c.214+62G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 1,524,528 control chromosomes in the GnomAD database, including 56,885 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 0.30 (6968 hom., cov: 33)
  • Exomes 𝑓: 0.27 (49917 hom.)
• Consequence: ADIPOQ NM_004797.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683
• Publications: 683 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004797.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOQ	NM_004797.4	MANE Select	c.214+62G>T		intron	N/A	NP_004788.1
	ADIPOQ	NM_001177800.2		c.214+62G>T		intron	N/A	NP_001171271.1
	ADIPOQ-AS1	NR_046662.2		n.2216-92C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOQ	ENST00000320741.7	TSL:1 MANE Select	c.214+62G>T		intron	N/A	ENSP00000320709.2
	ADIPOQ	ENST00000444204.2	TSL:1	c.214+62G>T		intron	N/A	ENSP00000389814.2
	ADIPOQ-AS1	ENST00000422718.1	TSL:5	n.2087-92C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45832 AN: 152038 Hom.: 6963 Cov.: 33

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.300

GnomAD4 exome AF: 0.267 AC: 366658 AN: 1372372 Hom.: 49917 AF XY: 0.265 AC XY: 180130 AN XY: 678606

African (AFR) AF: 0.365 AC: 11334 AN: 31076

American (AMR) AF: 0.278 AC: 9906 AN: 35666

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 7873 AN: 25036

East Asian (EAS) AF: 0.282 AC: 10038 AN: 35636

South Asian (SAS) AF: 0.226 AC: 17668 AN: 78338

European-Finnish (FIN) AF: 0.310 AC: 15262 AN: 49294

Middle Eastern (MID) AF: 0.306 AC: 1630 AN: 5324

European-Non Finnish (NFE) AF: 0.263 AC: 277317 AN: 1054976

Other (OTH) AF: 0.274 AC: 15630 AN: 57026

GnomAD4 genome AF: 0.301 AC: 45857 AN: 152156 Hom.: 6968 Cov.: 33 AF XY: 0.301 AC XY: 22388 AN XY: 74366

African (AFR) AF: 0.360 AC: 14930 AN: 41510

American (AMR) AF: 0.310 AC: 4740 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1032 AN: 3466

East Asian (EAS) AF: 0.284 AC: 1469 AN: 5168

South Asian (SAS) AF: 0.219 AC: 1058 AN: 4822

European-Finnish (FIN) AF: 0.312 AC: 3310 AN: 10596

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18369 AN: 67980

Other (OTH) AF: 0.299 AC: 633 AN: 2114

Alfa AF: 0.278 Hom.: 22656

Bravo AF: 0.302

Asia WGS AF: 0.281 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.57
DANN	Benign	0.48
PhyloP100		-0.68
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1501299; hg19: chr3-186571123; COSMIC: COSV57859563;