rs859267

Positions:

• chr17-15922707-A-C
• chr17-15922707-A-G

Variant summary

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

The XM_047435373.1(ADORA2B):​c.-377-17318A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0456 in 152,258 control chromosomes in the GnomAD database, including 381 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 0.046 (381 hom., cov: 32)
• Consequence: ADORA2B XM_047435373.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

Genes affected

ADORA2B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADORA2B	XM_047435373.1	c.-377-17318A>C		intron_variant
ADORA2B	XM_047435374.1	c.-377-17318A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0455 AC: 6928 AN: 152140 Hom.: 376 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0547

Gnomad ASJ AF: 0.00952

Gnomad EAS AF: 0.0169

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.0156

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00650

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0456 AC: 6948 AN: 152258 Hom.: 381 Cov.: 32 AF XY: 0.0470 AC XY: 3501 AN XY: 74460

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.0546

Gnomad4 ASJ AF: 0.00952

Gnomad4 EAS AF: 0.0168

Gnomad4 SAS AF: 0.0164

Gnomad4 FIN AF: 0.0156

Gnomad4 NFE AF: 0.00650

Gnomad4 OTH AF: 0.0308

Alfa AF: 0.0105 Hom.: 49

Bravo AF: 0.0499

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.41
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs859267; hg19: chr17-15826021;