rs2805562

Variant names:

• chr10-1325319-G-A
• rs2805562
• NM_018702.4:c.1077+37709C>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.1077+37709C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,942 control chromosomes in the GnomAD database, including 13,965 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 0.41 (13965 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADARB2	NM_018702.4	MANE Select	c.1077+37709C>T		intron	N/A	NP_061172.1	Q9NS39-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADARB2	ENST00000381312.6	TSL:1 MANE Select	c.1077+37709C>T		intron	N/A	ENSP00000370713.1	Q9NS39-1
	ENSG00000300765	ENST00000773909.1		n.67+2786C>T		intron	N/A
	ENSG00000300765	ENST00000773910.1		n.171+2642C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62349 AN: 151824 Hom.: 13944 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.411 AC: 62410 AN: 151942 Hom.: 13965 Cov.: 32 AF XY: 0.405 AC XY: 30069 AN XY: 74278

African (AFR) AF: 0.597 AC: 24736 AN: 41424

American (AMR) AF: 0.342 AC: 5220 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1466 AN: 3470

East Asian (EAS) AF: 0.185 AC: 954 AN: 5166

South Asian (SAS) AF: 0.216 AC: 1042 AN: 4814

European-Finnish (FIN) AF: 0.322 AC: 3395 AN: 10556

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24408 AN: 67920

Other (OTH) AF: 0.420 AC: 886 AN: 2108

Alfa AF: 0.370 Hom.: 6284

Bravo AF: 0.421

Asia WGS AF: 0.200 AC: 699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.89
PhyloP100		-0.22
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: rs2805562; hg19: chr10-1367514;