NM_018702.4:c.100+93738T>C

Variant names:

• chr10-1643313-A-G
• rs10903528
• NM_018702.4:c.100+93738T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018702.4(ADARB2):​c.100+93738T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,110 control chromosomes in the GnomAD database, including 44,586 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 0.73 (44586 hom., cov: 33)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018702.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADARB2	NM_018702.4	MANE Select	c.100+93738T>C		intron	N/A	NP_061172.1	Q9NS39-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADARB2	ENST00000381312.6	TSL:1 MANE Select	c.100+93738T>C		intron	N/A	ENSP00000370713.1	Q9NS39-1

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111554 AN: 151992 Hom.: 44586 Cov.: 33

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.734 AC: 111581 AN: 152110 Hom.: 44586 Cov.: 33 AF XY: 0.734 AC XY: 54563 AN XY: 74364

African (AFR) AF: 0.385 AC: 15965 AN: 41450

American (AMR) AF: 0.802 AC: 12261 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2829 AN: 3470

East Asian (EAS) AF: 0.857 AC: 4437 AN: 5178

South Asian (SAS) AF: 0.730 AC: 3517 AN: 4816

European-Finnish (FIN) AF: 0.854 AC: 9037 AN: 10584

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60840 AN: 68012

Other (OTH) AF: 0.771 AC: 1629 AN: 2112

Alfa AF: 0.823 Hom.: 30560

Bravo AF: 0.719

Asia WGS AF: 0.755 AC: 2626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.23
DANN	Benign	0.44
PhyloP100		-0.46
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10903528; hg19: chr10-1685508;