rs1874989

Positions:

• chr10-1717007-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.100+20044A>G		intron_variant		ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.100+20044A>G		intron_variant		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

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.423

Alfa AF: 0.362 Hom.: 5051

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1874989; hg19: chr10-1759201;