rs2804099

chr10-1314125-C-G

Variant summary

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

The NM_018702.4(ADARB2):c.1078-43056G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 152,108 control chromosomes in the GnomAD database, including 20,702 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 0.50 (20702 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADARB2	NM_018702.4	c.1078-43056G>C		intron_variant		ENST00000381312.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADARB2	ENST00000381312.6	c.1078-43056G>C		intron_variant		1	NM_018702.4	P1

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75788 AN: 151990 Hom.: 20663 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.499 AC: 75879 AN: 152108 Hom.: 20702 Cov.: 32 AF XY: 0.491 AC XY: 36500 AN XY: 74364

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.499

Alfa AF: 0.462 Hom.: 2150

Bravo AF: 0.511

Asia WGS AF: 0.333 AC: 1161 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	1.6
Dann	Benign	0.33

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: rs2804099; hg19: chr10-1356320;