rs1411187

chr8-131009717-G-A

Variant summary

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

The NM_001115.3(ADCY8):c.961-19175C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,192 control chromosomes in the GnomAD database, including 30,048 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 0.61 (30048 hom., cov: 34)
• Consequence: ADCY8 NM_001115.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADCY8	NM_001115.3	c.961-19175C>T		intron_variant		ENST00000286355.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADCY8	ENST00000286355.10	c.961-19175C>T		intron_variant		1	NM_001115.3	P1
ADCY8	ENST00000377928.7	c.961-19175C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92356 AN: 152072 Hom.: 29997 Cov.: 34

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.608 AC: 92473 AN: 152192 Hom.: 30048 Cov.: 34 AF XY: 0.611 AC XY: 45466 AN XY: 74394

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.558

Alfa AF: 0.522 Hom.: 10080

Bravo AF: 0.618

Asia WGS AF: 0.698 AC: 2423 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.6
Dann	Benign	0.50

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: rs1411187; hg19: chr8-132021963;