rs17826816

Variant names:

• chr5-7519185-A-G
• rs17826816
• NM_020546.3:c.409-1553A>G

Variant summary

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

The NM_020546.3(ADCY2):​c.409-1553A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,162 control chromosomes in the GnomAD database, including 2,798 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 (2798 hom., cov: 32)
• Consequence: ADCY2 NM_020546.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480
• Publications: 12 publications found

Genes affected

ADCY2 (HGNC:233): (adenylate cyclase 2) This gene encodes a member of the family of adenylate cyclases, which are membrane-associated enzymes that catalyze the formation of the secondary messenger cyclic adenosine monophosphate (cAMP). This enzyme is insensitive to Ca(2+)/calmodulin, and is stimulated by the G protein beta and gamma subunit complex. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020546.3. 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
	ADCY2	NM_020546.3	MANE Select	c.409-1553A>G		intron	N/A	NP_065433.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADCY2	ENST00000338316.9	TSL:1 MANE Select	c.409-1553A>G		intron	N/A	ENSP00000342952.4
	ADCY2	ENST00000484965.5	TSL:3	n.143-1553A>G		intron	N/A
	ADCY2	ENST00000498598.1	TSL:5	n.108-1553A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25642 AN: 152044 Hom.: 2799 Cov.: 32

Gnomad AFR AF: 0.0520

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.168 AC: 25639 AN: 152162 Hom.: 2798 Cov.: 32 AF XY: 0.166 AC XY: 12355 AN XY: 74388

African (AFR) AF: 0.0519 AC: 2155 AN: 41548

American (AMR) AF: 0.142 AC: 2176 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 797 AN: 3468

East Asian (EAS) AF: 0.00136 AC: 7 AN: 5160

South Asian (SAS) AF: 0.132 AC: 636 AN: 4822

European-Finnish (FIN) AF: 0.234 AC: 2481 AN: 10596

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16716 AN: 67962

Other (OTH) AF: 0.172 AC: 364 AN: 2112

Alfa AF: 0.211 Hom.: 5652

Bravo AF: 0.154

Asia WGS AF: 0.0530 AC: 182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.88
PhyloP100		0.48
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: rs17826816; hg19: chr5-7519298;