chr10-1429570-C-A

Position:

• chr10-1429570-C-A

Variant summary

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

The NM_018702.4(ADARB2):​c.101-50410G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,172 control chromosomes in the GnomAD database, including 1,829 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 (1829 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADARB2	NM_018702.4	c.101-50410G>T		intron_variant		ENST00000381312.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADARB2	ENST00000381312.6	c.101-50410G>T		intron_variant		1	NM_018702.4	P1

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20262 AN: 152054 Hom.: 1826 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0834

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.133 AC: 20272 AN: 152172 Hom.: 1829 Cov.: 32 AF XY: 0.134 AC XY: 9945 AN XY: 74410

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.0617

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0834

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0901 Hom.: 1552

Bravo AF: 0.131

Asia WGS AF: 0.195 AC: 676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.29
DANN	Benign	0.72

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: rs2820651; hg19: chr10-1471765;