10-1301531-A-G

Variant names:

• chr10-1301531-A-G
• rs10903420
• NM_018702.4:c.1078-30462T>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.1078-30462T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 151,902 control chromosomes in the GnomAD database, including 17,950 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 0.47 (17950 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625
• Publications: 4 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.1078-30462T>C		intron_variant	Intron 3 of 9	ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.1078-30462T>C		intron_variant	Intron 3 of 9	1	NM_018702.4	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70635 AN: 151784 Hom.: 17938 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.465 AC: 70674 AN: 151902 Hom.: 17950 Cov.: 32 AF XY: 0.473 AC XY: 35089 AN XY: 74206

African (AFR) AF: 0.272 AC: 11241 AN: 41388

American (AMR) AF: 0.574 AC: 8769 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1762 AN: 3470

East Asian (EAS) AF: 0.804 AC: 4148 AN: 5156

South Asian (SAS) AF: 0.705 AC: 3384 AN: 4802

European-Finnish (FIN) AF: 0.496 AC: 5231 AN: 10540

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.506 AC: 34374 AN: 67962

Other (OTH) AF: 0.492 AC: 1036 AN: 2106

Alfa AF: 0.507 Hom.: 10617

Bravo AF: 0.460

Asia WGS AF: 0.723 AC: 2511 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	3.8
DANN	Benign	0.67
PhyloP100		-0.63
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: rs10903420; hg19: chr10-1343726;