10-1588626-C-T

Position:

• chr10-1588626-C-T

Variant summary

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

The NM_018702.4(ADARB2):​c.100+148425G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 151,978 control chromosomes in the GnomAD database, including 41,588 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 0.74 (41588 hom., cov: 31)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.100+148425G>A		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+148425G>A		intron_variant		1	NM_018702.4	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111822 AN: 151860 Hom.: 41559 Cov.: 31

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.736 AC: 111906 AN: 151978 Hom.: 41588 Cov.: 31 AF XY: 0.738 AC XY: 54812 AN XY: 74298

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.745

Alfa AF: 0.763 Hom.: 85438

Bravo AF: 0.736

Asia WGS AF: 0.724 AC: 2518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.40
DANN	Benign	0.65

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: rs2999399; hg19: chr10-1630821;