chr5-7483798-T-C

Variant names:

• chr5-7483798-T-C
• rs1032719
• NM_020546.3:c.409-36940T>C

Variant summary

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

The NM_020546.3(ADCY2):​c.409-36940T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,084 control chromosomes in the GnomAD database, including 8,699 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 0.32 (8699 hom., cov: 32)
• Consequence: ADCY2 NM_020546.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 2 publications found

Genes affected

ADCY2 (HGNC:233): (adenylate cyclase 2) This gene encodes a member of the family of adenylate cyclases, which are membrane-associated enzymes that catalyze the formation of the secondary messenger cyclic adenosine monophosphate (cAMP). This enzyme is insensitive to Ca(2+)/calmodulin, and is stimulated by the G protein beta and gamma subunit complex. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADCY2	NM_020546.3	c.409-36940T>C		intron_variant	Intron 2 of 24	ENST00000338316.9	NP_065433.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADCY2	ENST00000338316.9	c.409-36940T>C		intron_variant	Intron 2 of 24	1	NM_020546.3	ENSP00000342952.4
ADCY2	ENST00000484965.5	n.143-36940T>C		intron_variant	Intron 1 of 2	3
ADCY2	ENST00000498598.1	n.108-36940T>C		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48806 AN: 151968 Hom.: 8673 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.321 AC: 48882 AN: 152084 Hom.: 8699 Cov.: 32 AF XY: 0.323 AC XY: 24030 AN XY: 74344

African (AFR) AF: 0.444 AC: 18391 AN: 41462

American (AMR) AF: 0.401 AC: 6126 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 959 AN: 3472

East Asian (EAS) AF: 0.531 AC: 2745 AN: 5170

South Asian (SAS) AF: 0.274 AC: 1318 AN: 4818

European-Finnish (FIN) AF: 0.239 AC: 2528 AN: 10578

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15770 AN: 67992

Other (OTH) AF: 0.321 AC: 677 AN: 2106

Alfa AF: 0.239 Hom.: 2705

Bravo AF: 0.342

Asia WGS AF: 0.429 AC: 1490 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	0.28
DANN	Benign	0.35
PhyloP100		-1.2
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: rs1032719; hg19: chr5-7483911;