rs3898610

Variant names:

• chr10-1442564-T-C
• rs3898610
• NM_018702.4:c.101-63404A>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.101-63404A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0811 in 152,234 control chromosomes in the GnomAD database, including 623 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 0.081 (623 hom., cov: 33)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54
• Publications: 5 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018702.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADARB2	NM_018702.4	MANE Select	c.101-63404A>G		intron	N/A	NP_061172.1	Q9NS39-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADARB2	ENST00000381312.6	TSL:1 MANE Select	c.101-63404A>G		intron	N/A	ENSP00000370713.1	Q9NS39-1

Frequencies

GnomAD3 genomes AF: 0.0811 AC: 12343 AN: 152116 Hom.: 622 Cov.: 33

Gnomad AFR AF: 0.0544

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0988

Gnomad ASJ AF: 0.0602

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.0487

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0792

Gnomad OTH AF: 0.0804

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

GnomAD4 genome AF: 0.0811 AC: 12346 AN: 152234 Hom.: 623 Cov.: 33 AF XY: 0.0842 AC XY: 6264 AN XY: 74434

African (AFR) AF: 0.0542 AC: 2254 AN: 41550

American (AMR) AF: 0.0991 AC: 1514 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0602 AC: 209 AN: 3472

East Asian (EAS) AF: 0.232 AC: 1205 AN: 5184

South Asian (SAS) AF: 0.0489 AC: 236 AN: 4826

European-Finnish (FIN) AF: 0.125 AC: 1320 AN: 10584

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0792 AC: 5387 AN: 68016

Other (OTH) AF: 0.0800 AC: 169 AN: 2112

Alfa AF: 0.0802 Hom.: 2130

Bravo AF: 0.0844

Asia WGS AF: 0.132 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.24
DANN	Benign	0.63
PhyloP100		-2.5
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: rs3898610; hg19: chr10-1484759;