10-1442564-T-C

Position:

• chr10-1442564-T-C

Variant summary

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

The NM_018702.4(ADARB2):​c.101-63404A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0811 in 152,234 control chromosomes in the GnomAD database, including 623 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 0.081 (623 hom., cov: 33)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADARB2	NM_018702.4	c.101-63404A>G		intron_variant		ENST00000381312.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADARB2	ENST00000381312.6	c.101-63404A>G		intron_variant		1	NM_018702.4	P1

Frequencies

GnomAD3 genomes AF: 0.0811 AC: 12343 AN: 152116 Hom.: 622 Cov.: 33

Gnomad AFR AF: 0.0544

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0988

Gnomad ASJ AF: 0.0602

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.0487

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0792

Gnomad OTH AF: 0.0804

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

GnomAD4 genome AF: 0.0811 AC: 12346 AN: 152234 Hom.: 623 Cov.: 33 AF XY: 0.0842 AC XY: 6264 AN XY: 74434

Gnomad4 AFR AF: 0.0542

Gnomad4 AMR AF: 0.0991

Gnomad4 ASJ AF: 0.0602

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.0489

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.0792

Gnomad4 OTH AF: 0.0800

Alfa AF: 0.0770 Hom.: 710

Bravo AF: 0.0844

Asia WGS AF: 0.132 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.24
DANN	Benign	0.63

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: rs3898610; hg19: chr10-1484759;