Variant rs3828628 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020546.3(ADCY2):c.570+71G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 1,576,390 control chromosomes in the GnomAD database, including 42,149 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 0.20 ( 3408 hom., cov: 32)

Exomes 𝑓: 0.23 ( 38741 hom. )

Consequence

ADCY2
NM_020546.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0490

Variant links:

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]

ADCY2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADCY2	NM_020546.3 link	c.570+71G>A		intron_variant		ENST00000338316.9	NP_065433.2	Q08462-1Q71UM8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
ADCY2	ENST00000338316.9 link	c.570+71G>A	intron_variant	1	NM_020546.3	ENSP00000342952.4	Q08462-1
ADCY2	ENST00000484965.5 link	n.304+71G>A	intron_variant	3
ADCY2	ENST00000498598.1 link	n.269+71G>A	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.200

AC:

30465

AN:

151978

Hom.:

3407

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.237

Gnomad AMR

AF:

0.183

Gnomad ASJ

AF:

0.207

Gnomad EAS

AF:

0.301

Gnomad SAS

AF:

0.336

Gnomad FIN

AF:

0.281

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.231

Gnomad OTH

AF:

0.200

GnomAD4 exome

AF:

0.229

AC:

326651

AN:

1424294

Hom.:

38741

AF XY:

0.234

AC XY:

165691

AN XY:

708166

show subpopulations

Gnomad4 AFR exome

AF:

0.103

Gnomad4 AMR exome

AF:

0.178

Gnomad4 ASJ exome

AF:

0.219

Gnomad4 EAS exome

AF:

0.338

Gnomad4 SAS exome

AF:

0.335

Gnomad4 FIN exome

AF:

0.279

Gnomad4 NFE exome

AF:

0.221

Gnomad4 OTH exome

AF:

0.230

GnomAD4 genome

AF:

0.200

AC:

30471

AN:

152096

Hom.:

3408

Cov.:

AF XY:

0.208

AC XY:

15441

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.106

Gnomad4 AMR

AF:

0.183

Gnomad4 ASJ

AF:

0.207

Gnomad4 EAS

AF:

0.301

Gnomad4 SAS

AF:

0.336

Gnomad4 FIN

AF:

0.281

Gnomad4 NFE

AF:

0.231

Gnomad4 OTH

AF:

0.199

Alfa

AF:

0.228

Hom.:

8212

Bravo

AF:

0.186

Asia WGS

AF:

0.294

AC:

1023

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.3

DANN

Benign

0.34

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over