chr10-1314125-C-G

Variant names:

• chr10-1314125-C-G
• rs2804099
• NM_018702.4:c.1078-43056G>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.1078-43056G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 152,108 control chromosomes in the GnomAD database, including 20,702 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 0.50 (20702 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.1078-43056G>C		intron_variant	Intron 3 of 9	ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.1078-43056G>C		intron_variant	Intron 3 of 9	1	NM_018702.4	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75788 AN: 151990 Hom.: 20663 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.499 AC: 75879 AN: 152108 Hom.: 20702 Cov.: 32 AF XY: 0.491 AC XY: 36500 AN XY: 74364

African (AFR) AF: 0.739 AC: 30676 AN: 41504

American (AMR) AF: 0.395 AC: 6039 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1630 AN: 3472

East Asian (EAS) AF: 0.297 AC: 1532 AN: 5164

South Asian (SAS) AF: 0.328 AC: 1579 AN: 4814

European-Finnish (FIN) AF: 0.371 AC: 3923 AN: 10586

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28988 AN: 67968

Other (OTH) AF: 0.499 AC: 1056 AN: 2116

Alfa AF: 0.462 Hom.: 2150

Bravo AF: 0.511

Asia WGS AF: 0.333 AC: 1161 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	1.6
DANN	Benign	0.33
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

Publications

LitVar

Other links and lift over

dbSNP: rs2804099; hg19: chr10-1356320;