rs4880511

Variant names:

• chr10-1488689-C-A
• rs4880511
• NM_018702.4:c.101-109529G>T

Variant summary

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

The NM_018702.4(ADARB2):​c.101-109529G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,248 control chromosomes in the GnomAD database, including 1,702 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 0.12 (1702 hom., cov: 33)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 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.101-109529G>T		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.101-109529G>T		intron	N/A	ENSP00000370713.1	Q9NS39-1

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17842 AN: 152130 Hom.: 1691 Cov.: 33

Gnomad AFR AF: 0.0467

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0974

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.117 AC: 17870 AN: 152248 Hom.: 1702 Cov.: 33 AF XY: 0.124 AC XY: 9238 AN XY: 74442

African (AFR) AF: 0.0467 AC: 1942 AN: 41564

American (AMR) AF: 0.296 AC: 4528 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 381 AN: 3472

East Asian (EAS) AF: 0.327 AC: 1690 AN: 5176

South Asian (SAS) AF: 0.194 AC: 935 AN: 4822

European-Finnish (FIN) AF: 0.129 AC: 1371 AN: 10612

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0974 AC: 6622 AN: 67994

Other (OTH) AF: 0.118 AC: 249 AN: 2116

Alfa AF: 0.112 Hom.: 2439

Bravo AF: 0.132

Asia WGS AF: 0.225 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.24
DANN	Benign	0.56
PhyloP100		-0.91
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: rs4880511; hg19: chr10-1530884;