ENST00000427813.6:n.1121+4585G>C

Variant names:

• chr22-24447626-C-G
• rs4822492
• ENST00000427813.6:n.1121+4585G>C

Variant summary

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

The ENST00000427813.6(ADORA2A-AS1):​n.1121+4585G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 152,052 control chromosomes in the GnomAD database, including 18,709 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 0.47 (18709 hom., cov: 32)
• Consequence: ADORA2A-AS1 ENST00000427813.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 29 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADORA2A-AS1	NR_028483.2	n.1121+4585G>C		intron_variant	Intron 5 of 7
ADORA2A-AS1	NR_028484.3	n.685-5486G>C		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADORA2A-AS1	ENST00000427813.6	n.1121+4585G>C		intron_variant	Intron 5 of 7	1
ADORA2A-AS1	ENST00000326341.8	n.411-5486G>C		intron_variant	Intron 3 of 6	5
ADORA2A-AS1	ENST00000412790.2	n.617-5486G>C		intron_variant	Intron 3 of 4	2

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72178 AN: 151934 Hom.: 18701 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.475 AC: 72207 AN: 152052 Hom.: 18709 Cov.: 32 AF XY: 0.472 AC XY: 35098 AN XY: 74306

African (AFR) AF: 0.265 AC: 10990 AN: 41478

American (AMR) AF: 0.525 AC: 8032 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1947 AN: 3472

East Asian (EAS) AF: 0.490 AC: 2529 AN: 5164

South Asian (SAS) AF: 0.320 AC: 1542 AN: 4822

European-Finnish (FIN) AF: 0.549 AC: 5797 AN: 10552

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39614 AN: 67962

Other (OTH) AF: 0.506 AC: 1068 AN: 2110

Alfa AF: 0.526 Hom.: 2732

Bravo AF: 0.473

Asia WGS AF: 0.391 AC: 1360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.41
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs4822492; hg19: chr22-24843594;