chr2-24907673-A-C

Position:

• chr2-24907673-A-C

Variant summary

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

The NM_004036.5(ADCY3):​c.675+10640T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 152,020 control chromosomes in the GnomAD database, including 22,856 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 0.52 (22856 hom., cov: 31)
• Consequence: ADCY3 NM_004036.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

Genes affected

ADCY3 (HGNC:234): (adenylate cyclase 3) This gene encodes adenylyl cyclase 3 which is a membrane-associated enzyme and catalyzes the formation of the secondary messenger cyclic adenosine monophosphate (cAMP). This protein appears to be widely expressed in various human tissues and may be involved in a number of physiological and pathophysiological metabolic processes. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADCY3	NM_004036.5	c.675+10640T>G		intron_variant		ENST00000679454.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADCY3	ENST00000679454.1	c.675+10640T>G		intron_variant			NM_004036.5	P4
ADCY3	ENST00000260600.9	c.675+10640T>G		intron_variant		1		P4
ADCY3	ENST00000405392.6	c.675+10640T>G		intron_variant		1		A1
ADCY3	ENST00000435135.5	c.675+10640T>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79201 AN: 151902 Hom.: 22814 Cov.: 31

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.522 AC: 79286 AN: 152020 Hom.: 22856 Cov.: 31 AF XY: 0.514 AC XY: 38184 AN XY: 74288

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.488

Alfa AF: 0.453 Hom.: 4604

Bravo AF: 0.530

Asia WGS AF: 0.436 AC: 1516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.37

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: rs10198275; hg19: chr2-25130542;