3-186856375-T-C

Variant names:

• chr3-186856375-T-C
• rs2082940
• NM_004797.4:c.*1671T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_004797.4(ADIPOQ):​c.*1671T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.85 in 152,152 control chromosomes in the GnomAD database, including 55,172 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 0.85 (55172 hom., cov: 34)
  • Failed GnomAD Quality Control
• Consequence: ADIPOQ NM_004797.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 47 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.885 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.*1671T>C		3_prime_UTR	Exon 3 of 3	NP_004788.1
	ADIPOQ	NM_001177800.2		c.*1671T>C		3_prime_UTR	Exon 4 of 4	NP_001171271.1
	ADIPOQ-AS1	NR_046662.2		n.137-259A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOQ	ENST00000320741.7	TSL:1 MANE Select	c.*1671T>C		3_prime_UTR	Exon 3 of 3	ENSP00000320709.2
	ADIPOQ	ENST00000444204.2	TSL:1	c.*1671T>C		3_prime_UTR	Exon 4 of 4	ENSP00000389814.2

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129214 AN: 152032 Hom.: 55160 Cov.: 34

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.957

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.814

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.850 AC: 129269 AN: 152152 Hom.: 55172 Cov.: 34 AF XY: 0.849 AC XY: 63154 AN XY: 74406

African (AFR) AF: 0.794 AC: 32936 AN: 41492

American (AMR) AF: 0.801 AC: 12234 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2765 AN: 3466

East Asian (EAS) AF: 0.709 AC: 3663 AN: 5168

South Asian (SAS) AF: 0.867 AC: 4187 AN: 4828

European-Finnish (FIN) AF: 0.957 AC: 10159 AN: 10618

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.891 AC: 60554 AN: 67982

Other (OTH) AF: 0.810 AC: 1710 AN: 2110

Alfa AF: 0.859 Hom.: 15520

Bravo AF: 0.836

Asia WGS AF: 0.777 AC: 2703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	9.3
DANN	Benign	0.91
PhyloP100		1.1
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: rs2082940; hg19: chr3-186574164;