rs12266914

Variant names:

• chr10-1191347-C-T
• rs12266914
• NM_018702.4:c.1865-6308G>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.1865-6308G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 152,086 control chromosomes in the GnomAD database, including 23,236 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 0.53 (23236 hom., cov: 33)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.1865-6308G>A		intron_variant	Intron 8 of 9	ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.1865-6308G>A		intron_variant	Intron 8 of 9	1	NM_018702.4	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81243 AN: 151968 Hom.: 23234 Cov.: 33

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.534 AC: 81262 AN: 152086 Hom.: 23236 Cov.: 33 AF XY: 0.537 AC XY: 39927 AN XY: 74348

African (AFR) AF: 0.309 AC: 12804 AN: 41490

American (AMR) AF: 0.529 AC: 8087 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2242 AN: 3472

East Asian (EAS) AF: 0.658 AC: 3396 AN: 5158

South Asian (SAS) AF: 0.670 AC: 3230 AN: 4824

European-Finnish (FIN) AF: 0.603 AC: 6379 AN: 10578

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43149 AN: 67964

Other (OTH) AF: 0.589 AC: 1243 AN: 2112

Alfa AF: 0.581 Hom.: 3317

Bravo AF: 0.520

Asia WGS AF: 0.643 AC: 2235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.31
DANN	Benign	0.58
PhyloP100		-1.9
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: rs12266914; hg19: chr10-1237287;