rs2444217

Variant names:

• chr16-3988386-G-A
• rs2444217
• NM_001116.4:c.2310+608C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-3988386-G-A
• chr16-3988386-G-C
• chr16-3988386-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001116.4(ADCY9):​c.2310+608C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 150,498 control chromosomes in the GnomAD database, including 17,704 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 0.46 (17704 hom., cov: 25)
• Consequence: ADCY9 NM_001116.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557
• Publications: 27 publications found

Genes affected

ADCY9 (HGNC:240): (adenylate cyclase 9) Adenylate cyclase is a membrane bound enzyme that catalyses the formation of cyclic AMP from ATP. It is regulated by a family of G protein-coupled receptors, protein kinases, and calcium. The type 9 adenylyl cyclase is a widely distributed adenylyl cyclase, and it is stimulated by beta-adrenergic receptor activation but is insensitive to forskolin, calcium, and somatostatin. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADCY9	NM_001116.4	c.2310+608C>T		intron_variant	Intron 6 of 10	ENST00000294016.8	NP_001107.2
ADCY9	XM_005255079.4	c.2367+608C>T		intron_variant	Intron 6 of 10		XP_005255136.1
ADCY9	XM_011522353.3	c.2367+608C>T		intron_variant	Intron 6 of 10		XP_011520655.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADCY9	ENST00000294016.8	c.2310+608C>T		intron_variant	Intron 6 of 10	1	NM_001116.4	ENSP00000294016.3
ADCY9	ENST00000576936.5	c.6+608C>T		intron_variant	Intron 1 of 5	5		ENSP00000460066.1
ADCY9	ENST00000575550.5	n.520+608C>T		intron_variant	Intron 4 of 4	4

Frequencies

GnomAD3 genomes AF: 0.457 AC: 68714 AN: 150382 Hom.: 17709 Cov.: 25

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.442

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.457 AC: 68706 AN: 150498 Hom.: 17704 Cov.: 25 AF XY: 0.457 AC XY: 33511 AN XY: 73360

African (AFR) AF: 0.219 AC: 8991 AN: 40988

American (AMR) AF: 0.425 AC: 6433 AN: 15134

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1559 AN: 3460

East Asian (EAS) AF: 0.543 AC: 2708 AN: 4990

South Asian (SAS) AF: 0.406 AC: 1924 AN: 4734

European-Finnish (FIN) AF: 0.626 AC: 6445 AN: 10302

Middle Eastern (MID) AF: 0.441 AC: 127 AN: 288

European-Non Finnish (NFE) AF: 0.577 AC: 39004 AN: 67608

Other (OTH) AF: 0.460 AC: 961 AN: 2090

Alfa AF: 0.523 Hom.: 60793

Bravo AF: 0.432

Asia WGS AF: 0.421 AC: 1461 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.76
PhyloP100		-0.56
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2444217; hg19: chr16-4038387;