rs1876898

Variant names:

• chr10-1204046-C-T
• rs1876898
• NM_018702.4:c.1683-3899G>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.1683-3899G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,026 control chromosomes in the GnomAD database, including 4,519 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 0.24 (4519 hom., cov: 31)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 6 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]

LINC00200 (HGNC:30974): (long intergenic non-protein coding RNA 200)

ENSG00000287043 (HGNC:):

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 = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.1683-3899G>A		intron_variant	Intron 7 of 9	ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.1683-3899G>A		intron_variant	Intron 7 of 9	1	NM_018702.4	ENSP00000370713.1
LINC00200	ENST00000655745.1	n.264+43409C>T		intron_variant	Intron 2 of 2
ENSG00000287043	ENST00000658498.1	n.325-2010G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35815 AN: 151908 Hom.: 4516 Cov.: 31

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.00522

Gnomad SAS AF: 0.0731

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.236 AC: 35834 AN: 152026 Hom.: 4519 Cov.: 31 AF XY: 0.231 AC XY: 17132 AN XY: 74324

African (AFR) AF: 0.247 AC: 10238 AN: 41460

American (AMR) AF: 0.194 AC: 2967 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 806 AN: 3470

East Asian (EAS) AF: 0.00542 AC: 28 AN: 5164

South Asian (SAS) AF: 0.0732 AC: 353 AN: 4824

European-Finnish (FIN) AF: 0.279 AC: 2945 AN: 10558

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17633 AN: 67950

Other (OTH) AF: 0.226 AC: 477 AN: 2110

Alfa AF: 0.237 Hom.: 812

Bravo AF: 0.230

Asia WGS AF: 0.0700 AC: 244 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	0.58
DANN	Benign	0.49
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1876898; hg19: chr10-1249986;