10-1329191-A-G

Variant names:

• chr10-1329191-A-G
• rs10903426
• NM_018702.4:c.1077+33837T>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.1077+33837T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 151,984 control chromosomes in the GnomAD database, including 17,518 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 0.47 (17518 hom., cov: 31)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187
• 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]

ENSG00000309582 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADARB2	NM_018702.4	MANE Select	c.1077+33837T>C		intron	N/A	NP_061172.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADARB2	ENST00000381312.6	TSL:1 MANE Select	c.1077+33837T>C		intron	N/A	ENSP00000370713.1
	ENSG00000309582	ENST00000842186.1		n.*178A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71188 AN: 151866 Hom.: 17480 Cov.: 31

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.469 AC: 71280 AN: 151984 Hom.: 17518 Cov.: 31 AF XY: 0.463 AC XY: 34435 AN XY: 74294

African (AFR) AF: 0.626 AC: 25927 AN: 41416

American (AMR) AF: 0.382 AC: 5835 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1640 AN: 3470

East Asian (EAS) AF: 0.301 AC: 1554 AN: 5170

South Asian (SAS) AF: 0.344 AC: 1655 AN: 4816

European-Finnish (FIN) AF: 0.390 AC: 4119 AN: 10552

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29108 AN: 67970

Other (OTH) AF: 0.476 AC: 1005 AN: 2112

Alfa AF: 0.343 Hom.: 1344

Bravo AF: 0.475

Asia WGS AF: 0.339 AC: 1180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.84
DANN	Benign	0.16
PhyloP100		-0.19
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: rs10903426; hg19: chr10-1371386;