rs2804097

Variant names:

• chr10-1319934-T-A
• rs2804097
• NM_018702.4:c.1077+43094A>T

Your query was ambiguous. Multiple possible variants found:

• chr10-1319934-T-A
• chr10-1319934-T-C
• chr10-1319934-T-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.1077+43094A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 152,108 control chromosomes in the GnomAD database, including 20,831 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 0.50 (20831 hom., cov: 33)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686
• 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]

ENSG00000300765 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.1077+43094A>T		intron_variant	Intron 3 of 9	ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.1077+43094A>T		intron_variant	Intron 3 of 9	1	NM_018702.4	ENSP00000370713.1
ENSG00000300765	ENST00000773909.1	n.248+123A>T		intron_variant	Intron 2 of 2
ENSG00000300765	ENST00000773910.1	n.352+123A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.500 AC: 76012 AN: 151990 Hom.: 20793 Cov.: 33

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.500 AC: 76101 AN: 152108 Hom.: 20831 Cov.: 33 AF XY: 0.492 AC XY: 36592 AN XY: 74346

African (AFR) AF: 0.743 AC: 30842 AN: 41492

American (AMR) AF: 0.395 AC: 6046 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1629 AN: 3466

East Asian (EAS) AF: 0.298 AC: 1540 AN: 5170

South Asian (SAS) AF: 0.329 AC: 1583 AN: 4818

European-Finnish (FIN) AF: 0.371 AC: 3917 AN: 10560

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29031 AN: 67994

Other (OTH) AF: 0.500 AC: 1056 AN: 2112

Alfa AF: 0.462 Hom.: 2150

Bravo AF: 0.513

Asia WGS AF: 0.334 AC: 1166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.44
DANN	Benign	0.69
PhyloP100		-0.69
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: rs2804097; hg19: chr10-1362129;