rs1023096

chr8-131023316-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001115.3(ADCY8):c.960+16058G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 152,080 control chromosomes in the GnomAD database, including 37,293 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 0.68 (37293 hom., cov: 32)
• Consequence: ADCY8 NM_001115.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADCY8	NM_001115.3	c.960+16058G>A		intron_variant		ENST00000286355.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADCY8	ENST00000286355.10	c.960+16058G>A		intron_variant		1	NM_001115.3	P1
ADCY8	ENST00000377928.7	c.960+16058G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103921 AN: 151960 Hom.: 37236 Cov.: 32

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.655

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.684 AC: 104040 AN: 152080 Hom.: 37293 Cov.: 32 AF XY: 0.687 AC XY: 51042 AN XY: 74330

Gnomad4 AFR AF: 0.906

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.654

Alfa AF: 0.605 Hom.: 12985

Bravo AF: 0.700

Asia WGS AF: 0.772 AC: 2683 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.24
Dann	Benign	0.46

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

Other links and lift over

dbSNP: rs1023096; hg19: chr8-132035562;