10-1648597-A-T

Variant names:

• chr10-1648597-A-T
• rs10794782
• NM_018702.4:c.100+88454T>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.100+88454T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 151,936 control chromosomes in the GnomAD database, including 17,066 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 0.47 (17066 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.514 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+88454T>A		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+88454T>A		intron	N/A	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71444 AN: 151818 Hom.: 17045 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.471 AC: 71512 AN: 151936 Hom.: 17066 Cov.: 32 AF XY: 0.474 AC XY: 35196 AN XY: 74226

African (AFR) AF: 0.508 AC: 21066 AN: 41430

American (AMR) AF: 0.412 AC: 6292 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1461 AN: 3472

East Asian (EAS) AF: 0.502 AC: 2598 AN: 5176

South Asian (SAS) AF: 0.531 AC: 2548 AN: 4800

European-Finnish (FIN) AF: 0.530 AC: 5560 AN: 10498

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.449 AC: 30485 AN: 67970

Other (OTH) AF: 0.455 AC: 962 AN: 2112

Alfa AF: 0.365 Hom.: 1087

Bravo AF: 0.459

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.45
PhyloP100		0.078
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: rs10794782; hg19: chr10-1690792;