rs2676192

chr10-1463279-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.101-84119G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 151,958 control chromosomes in the GnomAD database, including 26,870 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 0.59 (26870 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.909

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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADARB2	NM_018702.4	c.101-84119G>A		intron_variant		ENST00000381312.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADARB2	ENST00000381312.6	c.101-84119G>A		intron_variant		1	NM_018702.4	P1

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89817 AN: 151842 Hom.: 26840 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.592 AC: 89906 AN: 151958 Hom.: 26870 Cov.: 32 AF XY: 0.600 AC XY: 44521 AN XY: 74252

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.745

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.581

Alfa AF: 0.562 Hom.: 17025

Bravo AF: 0.590

Asia WGS AF: 0.720 AC: 2501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.1
Dann	Benign	0.51

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: rs2676192; hg19: chr10-1505474; COSMIC: COSV67235294;