rs10505566

Variant summary

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

The NM_001115.3(ADCY8):​c.2210+1024T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,090 control chromosomes in the GnomAD database, including 2,442 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 0.16 ( 2442 hom., cov: 32)

Consequence

ADCY8
NM_001115.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.176
Variant links:
Genes affected
ADCY8 (HGNC:239): (adenylate cyclase 8) Adenylate cyclase is a membrane bound enzyme that catalyses the formation of cyclic AMP from ATP. The enzymatic activity is under the control of several hormones, and different polypeptides participate in the transduction of the signal from the receptor to the catalytic moiety. Stimulatory or inhibitory receptors (Rs and Ri) interact with G proteins (Gs and Gi) that exhibit GTPase activity and they modulate the activity of the catalytic subunit of the adenylyl cyclase [provided by RefSeq, Jul 2008]

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=-0.85).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ADCY8NM_001115.3 linkuse as main transcriptc.2210+1024T>G intron_variant ENST00000286355.10 NP_001106.1
LOC105375762XR_928658.2 linkuse as main transcriptn.144+15743A>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ADCY8ENST00000286355.10 linkuse as main transcriptc.2210+1024T>G intron_variant 1 NM_001115.3 ENSP00000286355 P1
ADCY8ENST00000377928.7 linkuse as main transcriptc.2109+17742T>G intron_variant 1 ENSP00000367161

Frequencies

GnomAD3 genomes
AF:
0.164
AC:
24862
AN:
151972
Hom.:
2442
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0499
Gnomad AMI
AF:
0.251
Gnomad AMR
AF:
0.195
Gnomad ASJ
AF:
0.169
Gnomad EAS
AF:
0.181
Gnomad SAS
AF:
0.124
Gnomad FIN
AF:
0.191
Gnomad MID
AF:
0.117
Gnomad NFE
AF:
0.222
Gnomad OTH
AF:
0.146
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.164
AC:
24870
AN:
152090
Hom.:
2442
Cov.:
32
AF XY:
0.160
AC XY:
11858
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.0497
Gnomad4 AMR
AF:
0.195
Gnomad4 ASJ
AF:
0.169
Gnomad4 EAS
AF:
0.181
Gnomad4 SAS
AF:
0.125
Gnomad4 FIN
AF:
0.191
Gnomad4 NFE
AF:
0.222
Gnomad4 OTH
AF:
0.145
Alfa
AF:
0.199
Hom.:
5515
Bravo
AF:
0.157
Asia WGS
AF:
0.140
AC:
487
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
3.3
DANN
Benign
0.73

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.

Other links and lift over

dbSNP: rs10505566; hg19: chr8-131879068; API