rs859245

Variant names:

• chr17-15907248-G-A
• rs859245
• ENST00000421102.6:n.1075-1307G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421102.6(SPECC1P1):​n.1075-1307G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0851 in 151,784 control chromosomes in the GnomAD database, including 1,552 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 0.085 (1552 hom., cov: 32)
• Consequence: SPECC1P1 ENST00000421102.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351
• Publications: 0 publications found

Genes affected

SPECC1P1 (HGNC:53867): (SPECC1 pseudogene 1)

ENSG00000290377 (HGNC:):

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADORA2B	XM_047435373.1	c.-377-32777G>A		intron_variant	Intron 4 of 5		XP_047291329.1
ADORA2B	XM_047435374.1	c.-377-32777G>A		intron_variant	Intron 2 of 3		XP_047291330.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPECC1P1	ENST00000421102.6	n.1075-1307G>A		intron_variant	Intron 8 of 8	6
ENSG00000290377	ENST00000784729.1	n.258-32777G>A		intron_variant	Intron 2 of 2
ENSG00000290377	ENST00000784730.1	n.414-32777G>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.0849 AC: 12874 AN: 151666 Hom.: 1534 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0707

Gnomad ASJ AF: 0.00664

Gnomad EAS AF: 0.0172

Gnomad SAS AF: 0.0139

Gnomad FIN AF: 0.0153

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00644

Gnomad OTH AF: 0.0630

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

GnomAD4 genome AF: 0.0851 AC: 12922 AN: 151784 Hom.: 1552 Cov.: 32 AF XY: 0.0850 AC XY: 6302 AN XY: 74146

African (AFR) AF: 0.265 AC: 10927 AN: 41292

American (AMR) AF: 0.0705 AC: 1076 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.00664 AC: 23 AN: 3464

East Asian (EAS) AF: 0.0170 AC: 88 AN: 5176

South Asian (SAS) AF: 0.0137 AC: 66 AN: 4820

European-Finnish (FIN) AF: 0.0153 AC: 161 AN: 10496

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00644 AC: 438 AN: 67974

Other (OTH) AF: 0.0618 AC: 130 AN: 2102

Alfa AF: 0.0532 Hom.: 392

Bravo AF: 0.0946

Asia WGS AF: 0.0450 AC: 155 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	0.31
DANN	Benign	0.41
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs859245; hg19: chr17-15810562;