rs2387662

Positions:

• chr10-1384888-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018702.4(ADARB2):​c.101-5728G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,912 control chromosomes in the GnomAD database, including 11,648 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 0.38 (11648 hom., cov: 31)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADARB2	NM_018702.4	c.101-5728G>A		intron_variant		ENST00000381312.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADARB2	ENST00000381312.6	c.101-5728G>A		intron_variant		1	NM_018702.4	P1

Frequencies

GnomAD3 genomes AF: 0.382 AC: 57983 AN: 151794 Hom.: 11642 Cov.: 31

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.382 AC: 58002 AN: 151912 Hom.: 11648 Cov.: 31 AF XY: 0.380 AC XY: 28224 AN XY: 74246

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.405

Alfa AF: 0.432 Hom.: 6814

Bravo AF: 0.367

Asia WGS AF: 0.276 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.69

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

Publications

LitVar

Other links and lift over

dbSNP: rs2387662; hg19: chr10-1427083;