chr8-130795923-C-A

Variant summary

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

The NM_001115.3(ADCY8):​c.3060+4503G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0665 in 152,252 control chromosomes in the GnomAD database, including 471 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 0.066 ( 471 hom., cov: 32)

Consequence

ADCY8
NM_001115.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.83
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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.091 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ADCY8NM_001115.3 linkuse as main transcriptc.3060+4503G>T intron_variant ENST00000286355.10 NP_001106.1
ADCY8XM_005250769.4 linkuse as main transcriptc.2970+4503G>T intron_variant XP_005250826.1
ADCY8XM_006716501.4 linkuse as main transcriptc.2862+4503G>T intron_variant XP_006716564.1
ADCY8XM_017013006.2 linkuse as main transcriptc.2772+4503G>T intron_variant XP_016868495.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ADCY8ENST00000286355.10 linkuse as main transcriptc.3060+4503G>T intron_variant 1 NM_001115.3 ENSP00000286355 P1
ADCY8ENST00000377928.7 linkuse as main transcriptc.2667+4503G>T intron_variant 1 ENSP00000367161

Frequencies

GnomAD3 genomes
AF:
0.0665
AC:
10120
AN:
152134
Hom.:
471
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0162
Gnomad AMI
AF:
0.0154
Gnomad AMR
AF:
0.0691
Gnomad ASJ
AF:
0.0873
Gnomad EAS
AF:
0.00116
Gnomad SAS
AF:
0.0447
Gnomad FIN
AF:
0.134
Gnomad MID
AF:
0.0222
Gnomad NFE
AF:
0.0929
Gnomad OTH
AF:
0.0502
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0665
AC:
10118
AN:
152252
Hom.:
471
Cov.:
32
AF XY:
0.0658
AC XY:
4900
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.0161
Gnomad4 AMR
AF:
0.0691
Gnomad4 ASJ
AF:
0.0873
Gnomad4 EAS
AF:
0.000966
Gnomad4 SAS
AF:
0.0446
Gnomad4 FIN
AF:
0.134
Gnomad4 NFE
AF:
0.0929
Gnomad4 OTH
AF:
0.0497
Alfa
AF:
0.0853
Hom.:
852
Bravo
AF:
0.0614
Asia WGS
AF:
0.0210
AC:
73
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
0.32
DANN
Benign
0.70

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: rs263232; hg19: chr8-131808169; API