rs7627128

Variant names:

• chr3-186851010-C-A
• rs7627128
• NM_004797.4:c.-8-2041C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-186851010-C-A
• chr3-186851010-C-G

Variant summary

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

The NM_004797.4(ADIPOQ):​c.-8-2041C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 151,822 control chromosomes in the GnomAD database, including 2,276 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 0.17 (2276 hom., cov: 31)
• Consequence: ADIPOQ NM_004797.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.242
• Publications: 19 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 Gene-Disease associations (from GenCC):

• STAT3-related early-onset multisystem autoimmune disease

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

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 (EAS) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.-8-2041C>A		intron_variant	Intron 1 of 2	ENST00000320741.7	NP_004788.1
ADIPOQ	NM_001177800.2	c.-8-2041C>A		intron_variant	Intron 2 of 3		NP_001171271.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.-8-2041C>A		intron_variant	Intron 1 of 2	1	NM_004797.4	ENSP00000320709.2
ADIPOQ	ENST00000444204.2	c.-8-2041C>A		intron_variant	Intron 2 of 3	1		ENSP00000389814.2

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25745 AN: 151706 Hom.: 2273 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.170 AC: 25759 AN: 151822 Hom.: 2276 Cov.: 31 AF XY: 0.172 AC XY: 12738 AN XY: 74172

African (AFR) AF: 0.123 AC: 5100 AN: 41402

American (AMR) AF: 0.194 AC: 2954 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 717 AN: 3470

East Asian (EAS) AF: 0.238 AC: 1228 AN: 5162

South Asian (SAS) AF: 0.168 AC: 807 AN: 4814

European-Finnish (FIN) AF: 0.222 AC: 2334 AN: 10508

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.176 AC: 11972 AN: 67912

Other (OTH) AF: 0.165 AC: 348 AN: 2110

Alfa AF: 0.178 Hom.: 5544

Bravo AF: 0.171

Asia WGS AF: 0.217 AC: 755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.52
PhyloP100		0.24
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: rs7627128; hg19: chr3-186568799;