NM_018702.4:c.-5C>T

Variant names:

• chr10-1737155-G-A
• rs3750684
• NM_018702.4:c.-5C>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.-5C>T variant causes a 5 prime UTR premature start codon gain 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 NM_018702.4 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.00
• Publications: 12 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=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.55 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.-5C>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 10	NP_061172.1
	ADARB2	NM_018702.4	MANE Select	c.-5C>T		5_prime_UTR	Exon 1 of 10	NP_061172.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADARB2	ENST00000381312.6	TSL:1 MANE Select	c.-5C>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 10	ENSP00000370713.1
	ADARB2	ENST00000381312.6	TSL:1 MANE Select	c.-5C>T		5_prime_UTR	Exon 1 of 10	ENSP00000370713.1

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

GnomAD2 exomes AF: 0.496 AC: 120948 AN: 243712 AF XY: 0.504

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 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

African (AFR) AF: 0.509 AC: 17047 AN: 33462

American (AMR) AF: 0.444 AC: 19837 AN: 44712

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 15037 AN: 26120

East Asian (EAS) AF: 0.163 AC: 6472 AN: 39686

South Asian (SAS) AF: 0.531 AC: 45824 AN: 86250

European-Finnish (FIN) AF: 0.484 AC: 21904 AN: 45254

Middle Eastern (MID) AF: 0.544 AC: 3129 AN: 5748

European-Non Finnish (NFE) AF: 0.561 AC: 623284 AN: 1111686

Other (OTH) AF: 0.525 AC: 31693 AN: 60320

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

African (AFR) AF: 0.511 AC: 21222 AN: 41520

American (AMR) AF: 0.504 AC: 7703 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2042 AN: 3470

East Asian (EAS) AF: 0.155 AC: 802 AN: 5162

South Asian (SAS) AF: 0.529 AC: 2552 AN: 4824

European-Finnish (FIN) AF: 0.493 AC: 5223 AN: 10584

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37686 AN: 67964

Other (OTH) AF: 0.549 AC: 1160 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	13
DANN	Benign	0.84
PhyloP100		4.0
PromoterAI		-0.098	Neutral
Mutation Taster		=297/3	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3750684; hg19: chr10-1779349; COSMIC: COSV67221055;