rs10508213

Variant names:

• chr10-1568970-G-T
• rs10508213
• NM_018702.4:c.100+168081C>A

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+168081C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,208 control chromosomes in the GnomAD database, including 1,142 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 0.11 (1142 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.100+168081C>A		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+168081C>A		intron_variant	Intron 1 of 9	1	NM_018702.4	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16429 AN: 152090 Hom.: 1142 Cov.: 32

Gnomad AFR AF: 0.0284

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.0976

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.108 AC: 16419 AN: 152208 Hom.: 1142 Cov.: 32 AF XY: 0.108 AC XY: 8010 AN XY: 74418

African (AFR) AF: 0.0283 AC: 1176 AN: 41552

American (AMR) AF: 0.0973 AC: 1488 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 577 AN: 3468

East Asian (EAS) AF: 0.142 AC: 737 AN: 5184

South Asian (SAS) AF: 0.114 AC: 550 AN: 4820

European-Finnish (FIN) AF: 0.145 AC: 1540 AN: 10590

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9920 AN: 67990

Other (OTH) AF: 0.107 AC: 226 AN: 2104

Alfa AF: 0.133 Hom.: 2411

Bravo AF: 0.101

Asia WGS AF: 0.106 AC: 367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.74
PhyloP100		0.27
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: rs10508213; hg19: chr10-1611165;