rs5024862

Positions:

• chr10-1470351-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018702.4(ADARB2):​c.101-91191C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,114 control chromosomes in the GnomAD database, including 10,300 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 0.35 (10300 hom., cov: 34)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.101-91191C>T		intron_variant		ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.101-91191C>T		intron_variant		1	NM_018702.4	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53745 AN: 151996 Hom.: 10296 Cov.: 34

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.353 AC: 53767 AN: 152114 Hom.: 10300 Cov.: 34 AF XY: 0.356 AC XY: 26505 AN XY: 74358

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.364

Alfa AF: 0.403 Hom.: 16667

Bravo AF: 0.335

Asia WGS AF: 0.455 AC: 1581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.57

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: rs5024862; hg19: chr10-1512546;