22-24439072-CTTTTTTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTTTTTTTTTTTTT

Variant names:

• chr22-24439072-C-CTTTTTTTTT
• rs3032740
• NM_000675.6:c.333-1490_333-1482dupTTTTTTTTT

Variant summary

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

The NM_000675.6(ADORA2A):​c.333-1490_333-1482dupTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.011 (129 hom., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: ADORA2A NM_000675.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 11 publications found

Genes affected

ADORA2A (HGNC:263): (adenosine A2a receptor) This gene encodes a member of the guanine nucleotide-binding protein (G protein)-coupled receptor (GPCR) superfamily, which is subdivided into classes and subtypes. The receptors are seven-pass transmembrane proteins that respond to extracellular cues and activate intracellular signal transduction pathways. This protein, an adenosine receptor of A2A subtype, uses adenosine as the preferred endogenous agonist and preferentially interacts with the G(s) and G(olf) family of G proteins to increase intracellular cAMP levels. It plays an important role in many biological functions, such as cardiac rhythm and circulation, cerebral and renal blood flow, immune function, pain regulation, and sleep. It has been implicated in pathophysiological conditions such as inflammatory diseases and neurodegenerative disorders. Alternative splicing results in multiple transcript variants. A read-through transcript composed of the upstream SPECC1L (sperm antigen with calponin homology and coiled-coil domains 1-like) and ADORA2A (adenosine A2a receptor) gene sequence has been identified, but it is thought to be non-coding. [provided by RefSeq, Jun 2013]

SPECC1L-ADORA2A (HGNC:49185): (SPECC1L-ADORA2A readthrough (NMD candidate)) This locus represents naturally occurring readthrough transcription between the neighboring SPECC1L (sperm antigen with calponin homology and coiled-coil domains 1-like) and ADORA2A (adenosine A2a receptor) genes on chromosome 22. The readthrough transcript is a candidate for nonsense-mediated mRNA decay (NMD) and is unlikely to produce a protein product. [provided by RefSeq, Jun 2013]

ADORA2A-AS1 (HGNC:37122): (ADORA2A antisense RNA 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000675.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADORA2A	NM_000675.6	MANE Select	c.333-1490_333-1482dupTTTTTTTTT		intron	N/A	NP_000666.2
	ADORA2A	NM_001278497.2		c.333-1490_333-1482dupTTTTTTTTT		intron	N/A	NP_001265426.1	P29274
	ADORA2A	NM_001278498.2		c.333-1490_333-1482dupTTTTTTTTT		intron	N/A	NP_001265427.1	X5DNB4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADORA2A	ENST00000337539.12	TSL:1 MANE Select	c.333-1511_333-1510insTTTTTTTTT		intron	N/A	ENSP00000336630.6	P29274
	ADORA2A	ENST00000618076.3	TSL:1	c.333-1511_333-1510insTTTTTTTTT		intron	N/A	ENSP00000481552.1	P29274
	SPECC1L-ADORA2A	ENST00000358654.2	TSL:2	n.*1468-1511_*1468-1510insTTTTTTTTT		intron	N/A	ENSP00000351480.2	F8WAN1

Frequencies

GnomAD3 genomes AF: 0.0112 AC: 818 AN: 73092 Hom.: 129 Cov.: 20

Gnomad AFR AF: 0.00370

Gnomad AMI AF: 0.00916

Gnomad AMR AF: 0.00739

Gnomad ASJ AF: 0.0233

Gnomad EAS AF: 0.0153

Gnomad SAS AF: 0.00472

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0163

Gnomad OTH AF: 0.00552

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0112 AC: 818 AN: 73100 Hom.: 129 Cov.: 20 AF XY: 0.0101 AC XY: 331 AN XY: 32704

African (AFR) AF: 0.00370 AC: 82 AN: 22182

American (AMR) AF: 0.00739 AC: 37 AN: 5010

Ashkenazi Jewish (ASJ) AF: 0.0233 AC: 49 AN: 2102

East Asian (EAS) AF: 0.0154 AC: 26 AN: 1690

South Asian (SAS) AF: 0.00474 AC: 7 AN: 1478

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1786

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 112

European-Non Finnish (NFE) AF: 0.0163 AC: 607 AN: 37284

Other (OTH) AF: 0.00549 AC: 5 AN: 910

Alfa AF: 0.00626 Hom.: 98

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.052
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs3032740; hg19: chr22-24835040;