rs2535611

chr17-15958018-C-T

Variant summary

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

The NM_000676.4(ADORA2B):c.335+12435C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.961 in 148,694 control chromosomes in the GnomAD database, including 68,670 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 0.96 (68670 hom., cov: 27)
• Consequence: ADORA2B NM_000676.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72

Genes affected

ADORA2B (HGNC:264): (adenosine A2b receptor) This gene encodes an adenosine receptor that is a member of the G protein-coupled receptor superfamily. This integral membrane protein stimulates adenylate cyclase activity in the presence of adenosine. This protein also interacts with netrin-1, which is involved in axon elongation. The gene is located near the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.985 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADORA2B	NM_000676.4	c.335+12435C>T		intron_variant		ENST00000304222.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADORA2B	ENST00000304222.3	c.335+12435C>T		intron_variant		1	NM_000676.4	P1

Frequencies

GnomAD3 genomes AF: 0.961 AC: 142806 AN: 148622 Hom.: 68642 Cov.: 27

Gnomad AFR AF: 0.906

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.942

Gnomad ASJ AF: 0.970

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.978

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.969

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

GnomAD4 genome AF: 0.961 AC: 142870 AN: 148694 Hom.: 68670 Cov.: 27 AF XY: 0.959 AC XY: 69327 AN XY: 72278

Gnomad4 AFR AF: 0.906

Gnomad4 AMR AF: 0.942

Gnomad4 ASJ AF: 0.970

Gnomad4 EAS AF: 0.973

Gnomad4 SAS AF: 0.978

Gnomad4 FIN AF: 0.979

Gnomad4 NFE AF: 0.992

Gnomad4 OTH AF: 0.969

Alfa AF: 0.968 Hom.: 6901

Asia WGS AF: 0.900 AC: 2994 AN: 3324

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.10
Dann	Benign	0.52

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: rs2535611; hg19: chr17-15861332; COSMIC: COSV58483389;