NM_004036.5:c.2871A>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_004036.5(ADCY3):c.2871A>G(p.Ser957Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 1,611,864 control chromosomes in the GnomAD database, including 371,410 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.65 ( 32642 hom., cov: 32)
Exomes 𝑓: 0.68 ( 338768 hom. )
Consequence
ADCY3
NM_004036.5 synonymous
NM_004036.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.32
Publications
25 publications found
Genes affected
ADCY3 (HGNC:234): (adenylate cyclase 3) This gene encodes adenylyl cyclase 3 which is a membrane-associated enzyme and catalyzes the formation of the secondary messenger cyclic adenosine monophosphate (cAMP). This protein appears to be widely expressed in various human tissues and may be involved in a number of physiological and pathophysiological metabolic processes. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]
ADCY3 Gene-Disease associations (from GenCC):
- body mass index quantitative trait locus 19Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant 2-24823221-T-C is Benign according to our data. Variant chr2-24823221-T-C is described in ClinVar as [Benign]. Clinvar id is 1641173.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-4.32 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.650 AC: 98760AN: 151934Hom.: 32628 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
98760
AN:
151934
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.694 AC: 173780AN: 250322 AF XY: 0.690 show subpopulations
GnomAD2 exomes
AF:
AC:
173780
AN:
250322
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.679 AC: 991473AN: 1459812Hom.: 338768 Cov.: 51 AF XY: 0.679 AC XY: 492699AN XY: 726138 show subpopulations
GnomAD4 exome
AF:
AC:
991473
AN:
1459812
Hom.:
Cov.:
51
AF XY:
AC XY:
492699
AN XY:
726138
show subpopulations
African (AFR)
AF:
AC:
17478
AN:
33406
American (AMR)
AF:
AC:
37393
AN:
44438
Ashkenazi Jewish (ASJ)
AF:
AC:
17177
AN:
26112
East Asian (EAS)
AF:
AC:
34782
AN:
39666
South Asian (SAS)
AF:
AC:
58294
AN:
86080
European-Finnish (FIN)
AF:
AC:
35009
AN:
53390
Middle Eastern (MID)
AF:
AC:
3400
AN:
5058
European-Non Finnish (NFE)
AF:
AC:
746523
AN:
1111398
Other (OTH)
AF:
AC:
41417
AN:
60264
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.488
Heterozygous variant carriers
0
16874
33749
50623
67498
84372
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.650 AC: 98817AN: 152052Hom.: 32642 Cov.: 32 AF XY: 0.654 AC XY: 48611AN XY: 74328 show subpopulations
GnomAD4 genome
AF:
AC:
98817
AN:
152052
Hom.:
Cov.:
32
AF XY:
AC XY:
48611
AN XY:
74328
show subpopulations
African (AFR)
AF:
AC:
22180
AN:
41446
American (AMR)
AF:
AC:
11830
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
AC:
2233
AN:
3472
East Asian (EAS)
AF:
AC:
4527
AN:
5176
South Asian (SAS)
AF:
AC:
3343
AN:
4826
European-Finnish (FIN)
AF:
AC:
6914
AN:
10566
Middle Eastern (MID)
AF:
AC:
194
AN:
294
European-Non Finnish (NFE)
AF:
AC:
45590
AN:
67972
Other (OTH)
AF:
AC:
1450
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1755
3510
5266
7021
8776
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2713
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Feb 03, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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