rs1874989

Variant names:

• chr10-1717007-T-C
• rs1874989
• NM_018702.4:c.100+20044A>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.100+20044A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 151,904 control chromosomes in the GnomAD database, including 16,464 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 0.44 (16464 hom., cov: 31)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 1 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.100+20044A>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.100+20044A>G		intron_variant	Intron 1 of 9	1	NM_018702.4	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67301 AN: 151782 Hom.: 16436 Cov.: 31

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.443 AC: 67364 AN: 151904 Hom.: 16464 Cov.: 31 AF XY: 0.444 AC XY: 32930 AN XY: 74224

African (AFR) AF: 0.658 AC: 27214 AN: 41376

American (AMR) AF: 0.436 AC: 6656 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1633 AN: 3470

East Asian (EAS) AF: 0.303 AC: 1565 AN: 5164

South Asian (SAS) AF: 0.223 AC: 1074 AN: 4820

European-Finnish (FIN) AF: 0.427 AC: 4496 AN: 10536

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23293 AN: 67970

Other (OTH) AF: 0.423 AC: 890 AN: 2106

Alfa AF: 0.403 Hom.: 8557

Bravo AF: 0.456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.9
DANN	Benign	0.48
PhyloP100		0.0090
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: rs1874989; hg19: chr10-1759201;