10-1300822-C-T

Variant names:

• chr10-1300822-C-T
• rs11599315
• NM_018702.4:c.1078-29753G>A

Variant summary

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

The NM_018702.4(ADARB2):​c.1078-29753G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 152,132 control chromosomes in the GnomAD database, including 28,696 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 0.60 (28696 hom., cov: 33)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.1078-29753G>A		intron_variant	Intron 3 of 9	ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.1078-29753G>A		intron_variant	Intron 3 of 9	1	NM_018702.4	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90751 AN: 152014 Hom.: 28678 Cov.: 33

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.597 AC: 90809 AN: 152132 Hom.: 28696 Cov.: 33 AF XY: 0.605 AC XY: 44998 AN XY: 74386

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.618

Alfa AF: 0.643 Hom.: 43652

Bravo AF: 0.584

Asia WGS AF: 0.842 AC: 2925 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	2.1
DANN	Benign	0.20

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: rs11599315; hg19: chr10-1343017;