rs2805543

Variant names:

• chr10-1422697-T-C
• rs2805543
• NM_018702.4:c.101-43537A>G

Variant summary

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

The NM_018702.4(ADARB2):​c.101-43537A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,130 control chromosomes in the GnomAD database, including 15,738 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 0.42 (15738 hom., cov: 33)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 6 publications found

Genes affected

ADARB2 (HGNC:227): (adenosine deaminase RNA specific B2 (inactive)) This gene encodes a member of the double-stranded RNA adenosine deaminase family of RNA-editing enzymes and may play a regulatory role in RNA editing. [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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.101-43537A>G		intron_variant	Intron 1 of 9	ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.101-43537A>G		intron_variant	Intron 1 of 9	1	NM_018702.4	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64538 AN: 152012 Hom.: 15717 Cov.: 33

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.425 AC: 64609 AN: 152130 Hom.: 15738 Cov.: 33 AF XY: 0.428 AC XY: 31836 AN XY: 74370

African (AFR) AF: 0.643 AC: 26690 AN: 41492

American (AMR) AF: 0.403 AC: 6161 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1077 AN: 3472

East Asian (EAS) AF: 0.678 AC: 3504 AN: 5170

South Asian (SAS) AF: 0.465 AC: 2240 AN: 4822

European-Finnish (FIN) AF: 0.364 AC: 3860 AN: 10592

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20025 AN: 67970

Other (OTH) AF: 0.380 AC: 804 AN: 2116

Alfa AF: 0.347 Hom.: 34477

Bravo AF: 0.441

Asia WGS AF: 0.583 AC: 2023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.68
PhyloP100		-0.38
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2805543; hg19: chr10-1464892;