NM_004797.4:c.*1690T>C

Variant names:

• chr3-186856394-T-C
• rs1063538
• NM_004797.4:c.*1690T>C

Variant summary

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

The NM_004797.4(ADIPOQ):​c.*1690T>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 0.547 in 152,108 control chromosomes in the GnomAD database, including 23,399 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 0.55 (23399 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ADIPOQ NM_004797.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 32 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.626 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.*1690T>C		3_prime_UTR	Exon 3 of 3	NP_004788.1
	ADIPOQ	NM_001177800.2		c.*1690T>C		3_prime_UTR	Exon 4 of 4	NP_001171271.1
	ADIPOQ-AS1	NR_046662.2		n.137-278A>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.*1690T>C		3_prime_UTR	Exon 3 of 3	ENSP00000320709.2
	ADIPOQ	ENST00000444204.2	TSL:1	c.*1690T>C		3_prime_UTR	Exon 4 of 4	ENSP00000389814.2

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83227 AN: 151988 Hom.: 23384 Cov.: 33

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.511

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: 0.547 AC: 83263 AN: 152108 Hom.: 23399 Cov.: 33 AF XY: 0.547 AC XY: 40664 AN XY: 74354

African (AFR) AF: 0.433 AC: 17961 AN: 41476

American (AMR) AF: 0.490 AC: 7493 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1731 AN: 3464

East Asian (EAS) AF: 0.424 AC: 2191 AN: 5170

South Asian (SAS) AF: 0.645 AC: 3117 AN: 4830

European-Finnish (FIN) AF: 0.645 AC: 6831 AN: 10594

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42113 AN: 67960

Other (OTH) AF: 0.511 AC: 1079 AN: 2112

Alfa AF: 0.589 Hom.: 67582

Bravo AF: 0.533

Asia WGS AF: 0.495 AC: 1721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.55
PhyloP100		-0.18
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: rs1063538; hg19: chr3-186574183;