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rs11708067

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_183357.3(ADCY5):c.1406+851T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 151,998 control chromosomes in the GnomAD database, including 3,061 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 0.19 ( 3061 hom., cov: 31)

Consequence

ADCY5
NM_183357.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.42
Variant links:
Genes affected
ADCY5 (HGNC:236): (adenylate cyclase 5) This gene encodes a member of the membrane-bound adenylyl cyclase enzymes. Adenylyl cyclases mediate G protein-coupled receptor signaling through the synthesis of the second messenger cAMP. Activity of the encoded protein is stimulated by the Gs alpha subunit of G protein-coupled receptors and is inhibited by protein kinase A, calcium and Gi alpha subunits. Single nucleotide polymorphisms in this gene may be associated with low birth weight and type 2 diabetes. Alternatively spliced transcript variants that encode different isoforms have been observed for this gene. [provided by RefSeq, Dec 2010]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.25).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ADCY5NM_183357.3 linkuse as main transcriptc.1406+851T>C intron_variant ENST00000462833.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ADCY5ENST00000462833.6 linkuse as main transcriptc.1406+851T>C intron_variant 1 NM_183357.3 P1O95622-1

Frequencies

GnomAD3 genomes
AF:
0.193
AC:
29294
AN:
151878
Hom.:
3057
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.151
Gnomad AMI
AF:
0.183
Gnomad AMR
AF:
0.261
Gnomad ASJ
AF:
0.164
Gnomad EAS
AF:
0.00270
Gnomad SAS
AF:
0.198
Gnomad FIN
AF:
0.161
Gnomad MID
AF:
0.165
Gnomad NFE
AF:
0.225
Gnomad OTH
AF:
0.165
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.193
AC:
29310
AN:
151998
Hom.:
3061
Cov.:
31
AF XY:
0.189
AC XY:
14066
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.151
Gnomad4 AMR
AF:
0.261
Gnomad4 ASJ
AF:
0.164
Gnomad4 EAS
AF:
0.00271
Gnomad4 SAS
AF:
0.199
Gnomad4 FIN
AF:
0.161
Gnomad4 NFE
AF:
0.225
Gnomad4 OTH
AF:
0.162
Alfa
AF:
0.207
Hom.:
6331
Bravo
AF:
0.196
Asia WGS
AF:
0.0960
AC:
332
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.25
Cadd
Benign
17
Dann
Benign
0.69

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.060
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.

Other links and lift over

dbSNP: rs11708067; hg19: chr3-123065778; API