rs4880485

chr10-1181051-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADARB2	NM_018702.4	c.*2142T>C		3_prime_UTR_variant	10/10	ENST00000381312.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADARB2	ENST00000381312.6	c.*2142T>C		3_prime_UTR_variant	10/10	1	NM_018702.4	P1
LINC00200	ENST00000655745.1	n.264+20414A>G		intron_variant, non_coding_transcript_variant
LINC00200	ENST00000666348.1	n.243+20414A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.309

Alfa AF: 0.322 Hom.: 950

Bravo AF: 0.335

Asia WGS AF: 0.299 AC: 1042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
Dann	Benign	0.35

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: rs4880485; hg19: chr10-1226991;