rs3750684

Positions:

• chr10-1737155-G-A

Variant summary

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

The ENST00000381312.6(ADARB2):​c.-5C>T variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.538 in 1,605,374 control chromosomes in the GnomAD database, including 236,640 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 0.52 (21076 hom., cov: 33)
  • Exomes 𝑓: 0.54 (215564 hom.)
• Consequence: ADARB2 ENST00000381312.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.00

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=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.-5C>T		5_prime_UTR_variant	1/10	ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.-5C>T		5_prime_UTR_variant	1/10	1	NM_018702.4	ENSP00000370713	P1

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79135 AN: 152018 Hom.: 21065 Cov.: 33

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.549

GnomAD3 exomes AF: 0.496 AC: 120948 AN: 243712 Hom.: 31665 AF XY: 0.504 AC XY: 66884 AN XY: 132764

Gnomad AFR exome AF: 0.514

Gnomad AMR exome AF: 0.437

Gnomad ASJ exome AF: 0.577

Gnomad EAS exome AF: 0.153

Gnomad SAS exome AF: 0.527

Gnomad FIN exome AF: 0.488

Gnomad NFE exome AF: 0.552

Gnomad OTH exome AF: 0.528

GnomAD4 exome AF: 0.540 AC: 784227 AN: 1453238 Hom.: 215564 Cov.: 46 AF XY: 0.541 AC XY: 391029 AN XY: 723330

Gnomad4 AFR exome AF: 0.509

Gnomad4 AMR exome AF: 0.444

Gnomad4 ASJ exome AF: 0.576

Gnomad4 EAS exome AF: 0.163

Gnomad4 SAS exome AF: 0.531

Gnomad4 FIN exome AF: 0.484

Gnomad4 NFE exome AF: 0.561

Gnomad4 OTH exome AF: 0.525

GnomAD4 genome AF: 0.521 AC: 79188 AN: 152136 Hom.: 21076 Cov.: 33 AF XY: 0.514 AC XY: 38237 AN XY: 74378

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.549

Alfa AF: 0.538 Hom.: 5134

Bravo AF: 0.517

Asia WGS AF: 0.348 AC: 1216 AN: 3478

EpiCase AF: 0.557

EpiControl AF: 0.558

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	13
DANN	Benign	0.84

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3750684; hg19: chr10-1779349; COSMIC: COSV67221055;