10-1450612-A-G

Variant names:

• chr10-1450612-A-G
• rs2813427
• NM_018702.4:c.101-71452T>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.101-71452T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 152,178 control chromosomes in the GnomAD database, including 25,559 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 0.56 (25559 hom., cov: 34)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293
• 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=-0.97).
• 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.101-71452T>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.101-71452T>C		intron_variant	Intron 1 of 9	1	NM_018702.4	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84962 AN: 152060 Hom.: 25559 Cov.: 34

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.858

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.558 AC: 84991 AN: 152178 Hom.: 25559 Cov.: 34 AF XY: 0.558 AC XY: 41517 AN XY: 74394

African (AFR) AF: 0.327 AC: 13592 AN: 41514

American (AMR) AF: 0.556 AC: 8497 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2188 AN: 3472

East Asian (EAS) AF: 0.449 AC: 2320 AN: 5170

South Asian (SAS) AF: 0.566 AC: 2725 AN: 4818

European-Finnish (FIN) AF: 0.659 AC: 6978 AN: 10594

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46485 AN: 68008

Other (OTH) AF: 0.587 AC: 1238 AN: 2110

Alfa AF: 0.631 Hom.: 77401

Bravo AF: 0.535

Asia WGS AF: 0.465 AC: 1620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.47
DANN	Benign	0.56
PhyloP100		-0.29
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: rs2813427; hg19: chr10-1492807; COSMIC: COSV67220819;