rs4880801

chr10-1233561-T-G

Variant summary

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

The NM_018702.4(ADARB2):c.1513+133A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 941,770 control chromosomes in the GnomAD database, including 279,195 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 0.80 (49631 hom., cov: 32)
  • Exomes 𝑓: 0.76 (229564 hom.)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADARB2	NM_018702.4	c.1513+133A>C		intron_variant		ENST00000381312.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADARB2	ENST00000381312.6	c.1513+133A>C		intron_variant		1	NM_018702.4	P1
LINC00200	ENST00000655745.1	n.265-54912T>G		intron_variant, non_coding_transcript_variant
ADARB2	ENST00000469464.1	n.297+133A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122139 AN: 151982 Hom.: 49581 Cov.: 32

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.800

GnomAD4 exome AF: 0.759 AC: 599085 AN: 789670 Hom.: 229564 AF XY: 0.761 AC XY: 300355 AN XY: 394466

Gnomad4 AFR exome AF: 0.895

Gnomad4 AMR exome AF: 0.859

Gnomad4 ASJ exome AF: 0.763

Gnomad4 EAS exome AF: 0.992

Gnomad4 SAS exome AF: 0.915

Gnomad4 FIN exome AF: 0.719

Gnomad4 NFE exome AF: 0.732

Gnomad4 OTH exome AF: 0.777

GnomAD4 genome AF: 0.804 AC: 122246 AN: 152100 Hom.: 49631 Cov.: 32 AF XY: 0.806 AC XY: 59939 AN XY: 74342

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.927

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.799

Alfa AF: 0.779 Hom.: 5761

Bravo AF: 0.814

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.063

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4880801; hg19: chr10-1279503;