rs5024862

Variant names:

• chr10-1470351-G-A
• rs5024862
• NM_018702.4:c.101-91191C>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.101-91191C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,114 control chromosomes in the GnomAD database, including 10,300 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 0.35 (10300 hom., cov: 34)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.481 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.101-91191C>T		intron	N/A	NP_061172.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADARB2	ENST00000381312.6	TSL:1 MANE Select	c.101-91191C>T		intron	N/A	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53745 AN: 151996 Hom.: 10296 Cov.: 34

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.353 AC: 53767 AN: 152114 Hom.: 10300 Cov.: 34 AF XY: 0.356 AC XY: 26505 AN XY: 74358

African (AFR) AF: 0.201 AC: 8327 AN: 41506

American (AMR) AF: 0.311 AC: 4763 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1306 AN: 3470

East Asian (EAS) AF: 0.472 AC: 2433 AN: 5160

South Asian (SAS) AF: 0.498 AC: 2397 AN: 4814

European-Finnish (FIN) AF: 0.448 AC: 4733 AN: 10574

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28343 AN: 67986

Other (OTH) AF: 0.364 AC: 767 AN: 2106

Alfa AF: 0.394 Hom.: 20347

Bravo AF: 0.335

Asia WGS AF: 0.455 AC: 1581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.57
PhyloP100		-0.019
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: rs5024862; hg19: chr10-1512546;