10-1420963-G-C

Variant names:

• chr10-1420963-G-C
• rs4543904
• NM_018702.4:c.101-41803C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018702.4(ADARB2):​c.101-41803C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 151,744 control chromosomes in the GnomAD database, including 23,741 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 0.52 (23741 hom., cov: 30)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 8 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.101-41803C>G		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.101-41803C>G		intron_variant	Intron 1 of 9	1	NM_018702.4	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79602 AN: 151624 Hom.: 23741 Cov.: 30

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.525 AC: 79623 AN: 151744 Hom.: 23741 Cov.: 30 AF XY: 0.521 AC XY: 38649 AN XY: 74150

African (AFR) AF: 0.265 AC: 10968 AN: 41362

American (AMR) AF: 0.498 AC: 7573 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2423 AN: 3468

East Asian (EAS) AF: 0.194 AC: 997 AN: 5152

South Asian (SAS) AF: 0.548 AC: 2626 AN: 4788

European-Finnish (FIN) AF: 0.622 AC: 6546 AN: 10524

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46398 AN: 67926

Other (OTH) AF: 0.572 AC: 1203 AN: 2102

Alfa AF: 0.591 Hom.: 3541

Bravo AF: 0.501

Asia WGS AF: 0.361 AC: 1262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.57
DANN	Benign	0.47
PhyloP100		-1.2
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: rs4543904; hg19: chr10-1463158;