rs10903539

chr10-1674420-A-G

Variant summary

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

The NM_018702.4(ADARB2):c.100+62631T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,108 control chromosomes in the GnomAD database, including 6,639 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 0.27 (6639 hom., cov: 33)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADARB2	NM_018702.4	c.100+62631T>C		intron_variant		ENST00000381312.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADARB2	ENST00000381312.6	c.100+62631T>C		intron_variant		1	NM_018702.4	P1

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41547 AN: 151988 Hom.: 6634 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.273 AC: 41565 AN: 152108 Hom.: 6639 Cov.: 33 AF XY: 0.274 AC XY: 20354 AN XY: 74342

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.287

Alfa AF: 0.333 Hom.: 5672

Bravo AF: 0.263

Asia WGS AF: 0.213 AC: 742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.011
Dann	Benign	0.23

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: rs10903539; hg19: chr10-1716614;