10-1580229-A-G

Position:

• chr10-1580229-A-G

Variant summary

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

The NM_018702.4(ADARB2):​c.100+156822T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 151,970 control chromosomes in the GnomAD database, including 20,644 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 0.52 (20644 hom., cov: 31)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.78

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.100+156822T>C		intron_variant		ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.100+156822T>C		intron_variant		1	NM_018702.4	ENSP00000370713	P1

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78620 AN: 151852 Hom.: 20640 Cov.: 31

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.518 AC: 78663 AN: 151970 Hom.: 20644 Cov.: 31 AF XY: 0.523 AC XY: 38833 AN XY: 74232

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.530

Alfa AF: 0.522 Hom.: 2581

Bravo AF: 0.525

Asia WGS AF: 0.576 AC: 2001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.47

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: rs11815041; hg19: chr10-1622424;