NM_018702.4:c.1078-12147A>G

Variant names:

• chr10-1283216-T-C
• rs2804102
• NM_018702.4:c.1078-12147A>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.1078-12147A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 152,060 control chromosomes in the GnomAD database, including 23,433 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 0.55 (23433 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.06
• Publications: 3 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)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018702.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADARB2	NM_018702.4	MANE Select	c.1078-12147A>G		intron	N/A	NP_061172.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADARB2	ENST00000381312.6	TSL:1 MANE Select	c.1078-12147A>G		intron	N/A	ENSP00000370713.1
	LINC00200	ENST00000655745.1		n.265-5257T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83772 AN: 151942 Hom.: 23392 Cov.: 32

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.552 AC: 83876 AN: 152060 Hom.: 23433 Cov.: 32 AF XY: 0.556 AC XY: 41343 AN XY: 74330

African (AFR) AF: 0.539 AC: 22353 AN: 41472

American (AMR) AF: 0.618 AC: 9436 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1709 AN: 3468

East Asian (EAS) AF: 0.663 AC: 3425 AN: 5164

South Asian (SAS) AF: 0.767 AC: 3696 AN: 4818

European-Finnish (FIN) AF: 0.489 AC: 5170 AN: 10578

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36244 AN: 67960

Other (OTH) AF: 0.575 AC: 1216 AN: 2114

Alfa AF: 0.541 Hom.: 80896

Bravo AF: 0.553

Asia WGS AF: 0.733 AC: 2551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.097
DANN	Benign	0.64
PhyloP100		-3.1
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: rs2804102; hg19: chr10-1325411;