10-1648597-A-T

Position:

• chr10-1648597-A-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADARB2	NM_018702.4	c.100+88454T>A		intron_variant		ENST00000381312.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADARB2	ENST00000381312.6	c.100+88454T>A		intron_variant		1	NM_018702.4	P1

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

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.455

Alfa AF: 0.365 Hom.: 1087

Bravo AF: 0.459

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.45

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

Publications

LitVar

Other links and lift over

dbSNP: rs10794782; hg19: chr10-1690792;