rs4880487

Variant names:

• chr10-1200943-C-T
• rs4880487
• NM_018702.4:c.1683-796G>A

Variant summary

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

The NM_018702.4(ADARB2):​c.1683-796G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,098 control chromosomes in the GnomAD database, including 5,588 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 0.26 (5588 hom., cov: 33)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37
• Publications: 17 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]

LINC00200 (HGNC:30974): (long intergenic non-protein coding RNA 200)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADARB2	NM_018702.4	MANE Select	c.1683-796G>A		intron	N/A	NP_061172.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADARB2	ENST00000381312.6	TSL:1 MANE Select	c.1683-796G>A		intron	N/A	ENSP00000370713.1
	LINC00200	ENST00000655745.1		n.264+40306C>T		intron	N/A
	LINC00200	ENST00000666348.1		n.244-652C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39639 AN: 151980 Hom.: 5583 Cov.: 33

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.00519

Gnomad SAS AF: 0.0735

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.261 AC: 39666 AN: 152098 Hom.: 5588 Cov.: 33 AF XY: 0.255 AC XY: 18931 AN XY: 74328

African (AFR) AF: 0.342 AC: 14174 AN: 41482

American (AMR) AF: 0.203 AC: 3101 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 807 AN: 3472

East Asian (EAS) AF: 0.00540 AC: 28 AN: 5188

South Asian (SAS) AF: 0.0733 AC: 353 AN: 4814

European-Finnish (FIN) AF: 0.280 AC: 2957 AN: 10568

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17342 AN: 67978

Other (OTH) AF: 0.245 AC: 518 AN: 2114

Alfa AF: 0.251 Hom.: 16289

Bravo AF: 0.259

Asia WGS AF: 0.0780 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	11
DANN	Benign	0.70
PhyloP100		1.4
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: rs4880487; hg19: chr10-1246883;