rs4880801

Variant names:

• chr10-1233561-T-G
• rs4880801
• NM_018702.4:c.1513+133A>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.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
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADARB2	NM_018702.4	MANE Select	c.1513+133A>C		intron	N/A	NP_061172.1	Q9NS39-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADARB2	ENST00000381312.6	TSL:1 MANE Select	c.1513+133A>C		intron	N/A	ENSP00000370713.1	Q9NS39-1
	ADARB2	ENST00000469464.1	TSL:2	n.297+133A>C		intron	N/A
	LINC00200	ENST00000655745.1		n.265-54912T>G		intron	N/A

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

African (AFR) AF: 0.895 AC: 16522 AN: 18460

American (AMR) AF: 0.859 AC: 16510 AN: 19226

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 10911 AN: 14294

East Asian (EAS) AF: 0.992 AC: 30422 AN: 30670

South Asian (SAS) AF: 0.915 AC: 30374 AN: 33200

European-Finnish (FIN) AF: 0.719 AC: 31119 AN: 43306

Middle Eastern (MID) AF: 0.820 AC: 2070 AN: 2524

European-Non Finnish (NFE) AF: 0.732 AC: 433641 AN: 592562

Other (OTH) AF: 0.777 AC: 27516 AN: 35428

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

African (AFR) AF: 0.892 AC: 37011 AN: 41504

American (AMR) AF: 0.818 AC: 12502 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2664 AN: 3470

East Asian (EAS) AF: 0.995 AC: 5134 AN: 5162

South Asian (SAS) AF: 0.927 AC: 4474 AN: 4828

European-Finnish (FIN) AF: 0.717 AC: 7572 AN: 10566

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50378 AN: 67966

Other (OTH) AF: 0.799 AC: 1687 AN: 2112

Alfa AF: 0.779 Hom.: 5761

Bravo AF: 0.814

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.063
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs4880801; hg19: chr10-1279503;