chr10-1342438-G-A

Variant names:

• chr10-1342438-G-A
• rs2805533
• NM_018702.4:c.1077+20590C>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+20590C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,014 control chromosomes in the GnomAD database, including 22,056 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 (22056 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.535
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.1077+20590C>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+20590C>T		intron_variant	Intron 3 of 9	1	NM_018702.4	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80379 AN: 151896 Hom.: 22051 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.529 AC: 80400 AN: 152014 Hom.: 22056 Cov.: 32 AF XY: 0.534 AC XY: 39707 AN XY: 74326

African (AFR) AF: 0.369 AC: 15300 AN: 41456

American (AMR) AF: 0.616 AC: 9416 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1759 AN: 3468

East Asian (EAS) AF: 0.696 AC: 3593 AN: 5164

South Asian (SAS) AF: 0.656 AC: 3152 AN: 4802

European-Finnish (FIN) AF: 0.609 AC: 6441 AN: 10578

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38872 AN: 67944

Other (OTH) AF: 0.521 AC: 1102 AN: 2114

Alfa AF: 0.549 Hom.: 12388

Bravo AF: 0.523

Asia WGS AF: 0.663 AC: 2302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.67
PhyloP100		0.54
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: rs2805533; hg19: chr10-1384633;