chr5-7814229-T-TGAG

Variant names:

• chr5-7814229-T-TGAG
• rs2307998
• NM_020546.3:c.2884-2634_2884-2632dupGGA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_020546.3(ADCY2):​c.2884-2634_2884-2632dupGGA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: ADCY2 NM_020546.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456
• Publications: 3 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: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADCY2	NM_020546.3	c.2884-2634_2884-2632dupGGA		intron_variant	Intron 22 of 24	ENST00000338316.9	NP_065433.2
ADCY2	XM_047416645.1	c.2884-997_2884-995dupGGA		intron_variant	Intron 22 of 22		XP_047272601.1
ADCY2	XM_011513942.3	c.2746-2634_2746-2632dupGGA		intron_variant	Intron 21 of 23		XP_011512244.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADCY2	ENST00000338316.9	c.2884-2637_2884-2636insGAG		intron_variant	Intron 22 of 24	1	NM_020546.3	ENSP00000342952.4
ADCY2	ENST00000382531.7	n.595-2637_595-2636insGAG		intron_variant	Intron 5 of 5	5
ADCY2	ENST00000489501.1	n.8855-2637_8855-2636insGAG		intron_variant	Intron 2 of 4	2
ADCY2	ENST00000493243.5	n.*287-2637_*287-2636insGAG		intron_variant	Intron 5 of 6	5		ENSP00000426196.1

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2307998; hg19: chr5-7814342;