NM_018702.4:c.100+102715A>C

Variant names:

• chr10-1634336-T-G
• rs6560749
• NM_018702.4:c.100+102715A>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+102715A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.898 in 152,232 control chromosomes in the GnomAD database, including 62,118 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 0.90 (62118 hom., cov: 33)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 13 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 = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.100+102715A>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.100+102715A>C		intron_variant	Intron 1 of 9	1	NM_018702.4	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.899 AC: 136712 AN: 152114 Hom.: 62104 Cov.: 33

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.957

Gnomad FIN AF: 0.943

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.913

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

GnomAD4 genome AF: 0.898 AC: 136777 AN: 152232 Hom.: 62118 Cov.: 33 AF XY: 0.898 AC XY: 66840 AN XY: 74424

African (AFR) AF: 0.761 AC: 31591 AN: 41506

American (AMR) AF: 0.884 AC: 13526 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3120 AN: 3472

East Asian (EAS) AF: 0.879 AC: 4544 AN: 5172

South Asian (SAS) AF: 0.957 AC: 4622 AN: 4830

European-Finnish (FIN) AF: 0.943 AC: 10008 AN: 10610

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.974 AC: 66262 AN: 68032

Other (OTH) AF: 0.909 AC: 1917 AN: 2110

Alfa AF: 0.949 Hom.: 85488

Bravo AF: 0.887

Asia WGS AF: 0.878 AC: 3055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.023
DANN	Benign	0.35
PhyloP100		-1.2
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: rs6560749; hg19: chr10-1676531;