chr10-1364169-T-C

Variant names:

• chr10-1364169-T-C
• rs11250464
• NM_018702.4:c.188-252A>G

Variant summary

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

The NM_018702.4(ADARB2):​c.188-252A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,176 control chromosomes in the GnomAD database, including 6,711 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 0.28 (6711 hom., cov: 33)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 6 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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.188-252A>G		intron_variant	Intron 2 of 9	ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.188-252A>G		intron_variant	Intron 2 of 9	1	NM_018702.4	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42577 AN: 152058 Hom.: 6714 Cov.: 33

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.280 AC: 42587 AN: 152176 Hom.: 6711 Cov.: 33 AF XY: 0.277 AC XY: 20586 AN XY: 74404

African (AFR) AF: 0.188 AC: 7817 AN: 41522

American (AMR) AF: 0.256 AC: 3919 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1663 AN: 3470

East Asian (EAS) AF: 0.00347 AC: 18 AN: 5184

South Asian (SAS) AF: 0.221 AC: 1067 AN: 4818

European-Finnish (FIN) AF: 0.314 AC: 3324 AN: 10590

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23725 AN: 67966

Other (OTH) AF: 0.317 AC: 670 AN: 2114

Alfa AF: 0.317 Hom.: 10146

Bravo AF: 0.268

Asia WGS AF: 0.109 AC: 380 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	1.5
DANN	Benign	0.50
PhyloP100		-0.028
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: rs11250464; hg19: chr10-1406364;