rs3898609

chr10-1442527-C-Achr10-1442527-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.101-63367G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 152,146 control chromosomes in the GnomAD database, including 9,356 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 0.32 (9356 hom., cov: 33)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.784

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADARB2	NM_018702.4	c.101-63367G>T		intron_variant		ENST00000381312.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADARB2	ENST00000381312.6	c.101-63367G>T		intron_variant		1	NM_018702.4	P1

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49332 AN: 152028 Hom.: 9352 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.324 AC: 49344 AN: 152146 Hom.: 9356 Cov.: 33 AF XY: 0.327 AC XY: 24325 AN XY: 74378

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.317

Alfa AF: 0.222 Hom.: 660

Bravo AF: 0.311

Asia WGS AF: 0.303 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.1
Dann	Benign	0.39

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: rs3898609; hg19: chr10-1484722;