chr10-1524912-A-G

Variant names:

• chr10-1524912-A-G
• rs7905434
• NM_018702.4:c.101-145752T>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.101-145752T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,036 control chromosomes in the GnomAD database, including 8,939 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 0.33 (8939 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618
• Publications: 2 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.101-145752T>C		intron_variant	Intron 1 of 9	ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.101-145752T>C		intron_variant	Intron 1 of 9	1	NM_018702.4	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49399 AN: 151918 Hom.: 8933 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.325 AC: 49423 AN: 152036 Hom.: 8939 Cov.: 32 AF XY: 0.321 AC XY: 23816 AN XY: 74286

African (AFR) AF: 0.184 AC: 7616 AN: 41478

American (AMR) AF: 0.267 AC: 4079 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1228 AN: 3470

East Asian (EAS) AF: 0.198 AC: 1025 AN: 5168

South Asian (SAS) AF: 0.300 AC: 1445 AN: 4818

European-Finnish (FIN) AF: 0.411 AC: 4334 AN: 10546

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28616 AN: 67962

Other (OTH) AF: 0.315 AC: 665 AN: 2110

Alfa AF: 0.389 Hom.: 29990

Bravo AF: 0.308

Asia WGS AF: 0.256 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.86
PhyloP100		0.62
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: rs7905434; hg19: chr10-1567107;