rs4880485

Variant names:

• chr10-1181051-A-G
• rs4880485
• NM_018702.4:c.*2142T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018702.4(ADARB2):​c.*2142T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,176 control chromosomes in the GnomAD database, including 8,556 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 0.33 (8556 hom., cov: 34)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: ADARB2 NM_018702.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 2 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]

LINC00200 (HGNC:30974): (long intergenic non-protein coding RNA 200)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.391 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.*2142T>C		3_prime_UTR	Exon 10 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.*2142T>C		3_prime_UTR	Exon 10 of 10	ENSP00000370713.1
	LINC00200	ENST00000655745.1		n.264+20414A>G		intron	N/A
	LINC00200	ENST00000666348.1		n.243+20414A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50815 AN: 152046 Hom.: 8544 Cov.: 34

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.308

GnomAD4 exome AF: 0.250 AC: 3 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.300 AC XY: 3 AN XY: 10

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 1 AN: 6

Other (OTH) AF: 0.00 AC: 0 AN: 2

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.00109982), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.334 AC: 50868 AN: 152164 Hom.: 8556 Cov.: 34 AF XY: 0.336 AC XY: 24974 AN XY: 74372

African (AFR) AF: 0.342 AC: 14194 AN: 41504

American (AMR) AF: 0.399 AC: 6108 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 952 AN: 3472

East Asian (EAS) AF: 0.294 AC: 1526 AN: 5188

South Asian (SAS) AF: 0.308 AC: 1482 AN: 4818

European-Finnish (FIN) AF: 0.356 AC: 3771 AN: 10582

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21743 AN: 67988

Other (OTH) AF: 0.309 AC: 653 AN: 2112

Alfa AF: 0.323 Hom.: 997

Bravo AF: 0.335

Asia WGS AF: 0.299 AC: 1042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.35
PhyloP100		-1.4

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: rs4880485; hg19: chr10-1226991;