rs2805562

Positions:

• chr10-1325319-G-A

Variant summary

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

The NM_018702.4(ADARB2):​c.1077+37709C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,942 control chromosomes in the GnomAD database, including 13,965 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 0.41 (13965 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADARB2	NM_018702.4	c.1077+37709C>T		intron_variant		ENST00000381312.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADARB2	ENST00000381312.6	c.1077+37709C>T		intron_variant		1	NM_018702.4	P1

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62349 AN: 151824 Hom.: 13944 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.411 AC: 62410 AN: 151942 Hom.: 13965 Cov.: 32 AF XY: 0.405 AC XY: 30069 AN XY: 74278

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.420

Alfa AF: 0.370 Hom.: 5750

Bravo AF: 0.421

Asia WGS AF: 0.200 AC: 699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.89

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: rs2805562; hg19: chr10-1367514;