rs10903539

Variant names:

• chr10-1674420-A-G
• rs10903539
• NM_018702.4:c.100+62631T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.100+62631T>C		intron_variant	Intron 1 of 9	ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.100+62631T>C		intron_variant	Intron 1 of 9	1	NM_018702.4	ENSP00000370713.1

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

African (AFR) AF: 0.108 AC: 4466 AN: 41526

American (AMR) AF: 0.275 AC: 4195 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1228 AN: 3472

East Asian (EAS) AF: 0.191 AC: 987 AN: 5170

South Asian (SAS) AF: 0.282 AC: 1361 AN: 4824

European-Finnish (FIN) AF: 0.357 AC: 3765 AN: 10558

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24515 AN: 67970

Other (OTH) AF: 0.287 AC: 604 AN: 2104

Alfa AF: 0.309 Hom.: 8252

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
PhyloP100		-3.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10903539; hg19: chr10-1716614;