rs2676776

Variant names:

• chr10-1527891-T-C
• rs2676776
• NM_018702.4:c.101-148731A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-1527891-T-C
• chr10-1527891-T-G

Variant summary

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

The NM_018702.4(ADARB2):​c.101-148731A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,030 control chromosomes in the GnomAD database, including 25,320 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 0.57 (25320 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.624
• Publications: 7 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]

ADARB2-AS1 (HGNC:23299): (ADARB2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.101-148731A>G		intron_variant	Intron 1 of 9	ENST00000381312.6	NP_061172.1
ADARB2-AS1	NR_033387.2	n.270+992T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.101-148731A>G		intron_variant	Intron 1 of 9	1	NM_018702.4	ENSP00000370713.1
ADARB2-AS1	ENST00000421697.2	n.263+992T>C		intron_variant	Intron 1 of 1	1
ADARB2-AS1	ENST00000784177.1	n.453T>C		non_coding_transcript_exon_variant	Exon 2 of 2
ADARB2-AS1	ENST00000381301.3	n.137+992T>C		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86503 AN: 151912 Hom.: 25293 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.562

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.569 AC: 86576 AN: 152030 Hom.: 25320 Cov.: 32 AF XY: 0.570 AC XY: 42392 AN XY: 74328

African (AFR) AF: 0.451 AC: 18694 AN: 41440

American (AMR) AF: 0.639 AC: 9765 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2141 AN: 3470

East Asian (EAS) AF: 0.758 AC: 3921 AN: 5170

South Asian (SAS) AF: 0.625 AC: 3012 AN: 4816

European-Finnish (FIN) AF: 0.595 AC: 6282 AN: 10566

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40810 AN: 67980

Other (OTH) AF: 0.565 AC: 1188 AN: 2104

Alfa AF: 0.589 Hom.: 13131

Bravo AF: 0.571

Asia WGS AF: 0.681 AC: 2364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	12
DANN	Benign	0.50
PhyloP100		0.62
Mutation Taster		=100/0	polymorphism (auto)

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: rs2676776; hg19: chr10-1570086;