10-1208453-G-T

Variant names:

• chr10-1208453-G-T
• rs4880789
• NM_018702.4:c.1683-8306C>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.1683-8306C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,188 control chromosomes in the GnomAD database, including 5,837 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 0.27 (5837 hom., cov: 34)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.945
• Publications: 3 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)

ENSG00000287043 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.345 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.1683-8306C>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.1683-8306C>A		intron	N/A	ENSP00000370713.1
	LINC00200	ENST00000655745.1		n.264+47816G>T		intron	N/A
	ENSG00000287043	ENST00000658498.1		n.-64C>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40442 AN: 152070 Hom.: 5832 Cov.: 34

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.00521

Gnomad SAS AF: 0.0727

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.266 AC: 40470 AN: 152188 Hom.: 5837 Cov.: 34 AF XY: 0.260 AC XY: 19310 AN XY: 74412

African (AFR) AF: 0.350 AC: 14536 AN: 41520

American (AMR) AF: 0.207 AC: 3161 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 806 AN: 3470

East Asian (EAS) AF: 0.00541 AC: 28 AN: 5174

South Asian (SAS) AF: 0.0725 AC: 350 AN: 4826

European-Finnish (FIN) AF: 0.280 AC: 2966 AN: 10602

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17702 AN: 67970

Other (OTH) AF: 0.250 AC: 529 AN: 2114

Alfa AF: 0.130 Hom.: 224

Bravo AF: 0.265

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.63
DANN	Benign	0.56
PhyloP100		-0.94
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: rs4880789; hg19: chr10-1254393; COSMIC: COSV67235260;