rs2813400

chr10-1600803-A-C

Variant summary

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

The NM_018702.4(ADARB2):c.100+136248T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,042 control chromosomes in the GnomAD database, including 1,525 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 0.13 (1525 hom., cov: 31)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADARB2	NM_018702.4	c.100+136248T>G		intron_variant		ENST00000381312.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADARB2	ENST00000381312.6	c.100+136248T>G		intron_variant		1	NM_018702.4	P1

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19313 AN: 151926 Hom.: 1525 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.0308

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.0727

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0775

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.127 AC: 19344 AN: 152042 Hom.: 1525 Cov.: 31 AF XY: 0.130 AC XY: 9657 AN XY: 74356

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.0579

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.0721

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.0775

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0883 Hom.: 818

Bravo AF: 0.136

Asia WGS AF: 0.193 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.65
Dann	Benign	0.48

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: rs2813400; hg19: chr10-1642998;