chr17-15966243-G-T

Position:

• chr17-15966243-G-T

Variant summary

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

The NM_000676.4(ADORA2B):​c.336-8436G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0498 in 152,296 control chromosomes in the GnomAD database, including 205 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 0.050 (205 hom., cov: 33)
• Consequence: ADORA2B NM_000676.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADORA2B	NM_000676.4	c.336-8436G>T		intron_variant		ENST00000304222.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADORA2B	ENST00000304222.3	c.336-8436G>T		intron_variant		1	NM_000676.4	P1

Frequencies

GnomAD3 genomes AF: 0.0498 AC: 7573 AN: 152178 Hom.: 204 Cov.: 33

Gnomad AFR AF: 0.0723

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0458

Gnomad ASJ AF: 0.0282

Gnomad EAS AF: 0.0743

Gnomad SAS AF: 0.0600

Gnomad FIN AF: 0.0439

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0370

Gnomad OTH AF: 0.0531

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

GnomAD4 genome AF: 0.0498 AC: 7586 AN: 152296 Hom.: 205 Cov.: 33 AF XY: 0.0506 AC XY: 3766 AN XY: 74464

Gnomad4 AFR AF: 0.0724

Gnomad4 AMR AF: 0.0458

Gnomad4 ASJ AF: 0.0282

Gnomad4 EAS AF: 0.0745

Gnomad4 SAS AF: 0.0605

Gnomad4 FIN AF: 0.0439

Gnomad4 NFE AF: 0.0370

Gnomad4 OTH AF: 0.0520

Alfa AF: 0.0490 Hom.: 29

Bravo AF: 0.0512

Asia WGS AF: 0.0540 AC: 190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.55

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: rs17715109; hg19: chr17-15869557;