rs10794730

chr10-1201082-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.1683-935A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 152,192 control chromosomes in the GnomAD database, including 35,135 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 0.65 (35135 hom., cov: 33)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.29

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]

LINC00200 (HGNC:30974): (long intergenic non-protein coding RNA 200)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADARB2	NM_018702.4	c.1683-935A>G		intron_variant		ENST00000381312.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADARB2	ENST00000381312.6	c.1683-935A>G		intron_variant		1	NM_018702.4	P1
LINC00200	ENST00000655745.1	n.264+40445T>C		intron_variant, non_coding_transcript_variant
LINC00200	ENST00000666348.1	n.244-513T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.651 AC: 99010 AN: 152074 Hom.: 35120 Cov.: 33

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.651 AC: 99073 AN: 152192 Hom.: 35135 Cov.: 33 AF XY: 0.660 AC XY: 49141 AN XY: 74420

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.924

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.696

Alfa AF: 0.719 Hom.: 20966

Bravo AF: 0.640

Asia WGS AF: 0.907 AC: 3153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
Cadd	Benign	19
Dann	Benign	0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs10794730; hg19: chr10-1247022;