rs11815041

Variant names:

• chr10-1580229-A-G
• rs11815041
• NM_018702.4:c.100+156822T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-1580229-A-G
• chr10-1580229-A-T

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+156822T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 151,970 control chromosomes in the GnomAD database, including 20,644 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 0.52 (20644 hom., cov: 31)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.78
• Publications: 2 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 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.100+156822T>C		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.100+156822T>C		intron	N/A	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78620 AN: 151852 Hom.: 20640 Cov.: 31

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.518 AC: 78663 AN: 151970 Hom.: 20644 Cov.: 31 AF XY: 0.523 AC XY: 38833 AN XY: 74232

African (AFR) AF: 0.454 AC: 18798 AN: 41442

American (AMR) AF: 0.608 AC: 9294 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2119 AN: 3470

East Asian (EAS) AF: 0.638 AC: 3293 AN: 5160

South Asian (SAS) AF: 0.524 AC: 2515 AN: 4802

European-Finnish (FIN) AF: 0.595 AC: 6277 AN: 10544

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34704 AN: 67952

Other (OTH) AF: 0.530 AC: 1118 AN: 2108

Alfa AF: 0.522 Hom.: 2581

Bravo AF: 0.525

Asia WGS AF: 0.576 AC: 2001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.47
PhyloP100		-2.8
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: rs11815041; hg19: chr10-1622424;