rs4822492

Positions:

• chr22-24447626-C-G

Variant summary

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

The NR_028484.3(ADORA2A-AS1):​n.685-5486G>C variant causes a intron, non coding transcript 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 NR_028484.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ADORA2A-AS1	NR_028484.3	n.685-5486G>C		intron_variant, non_coding_transcript_variant
ADORA2A-AS1	NR_028483.2	n.1121+4585G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADORA2A-AS1	ENST00000326341.8	n.411-5486G>C		intron_variant, non_coding_transcript_variant		5
ADORA2A-AS1	ENST00000427813.6	n.1121+4585G>C		intron_variant, non_coding_transcript_variant		1
ADORA2A-AS1	ENST00000412790.2	n.617-5486G>C		intron_variant, non_coding_transcript_variant		2
ADORA2A-AS1	ENST00000650766.1	n.730-5486G>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.506

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4822492; hg19: chr22-24843594;