10-1611074-C-G

Variant names:

• chr10-1611074-C-G
• rs1874993
• NM_018702.4:c.100+125977G>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+125977G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 151,984 control chromosomes in the GnomAD database, including 26,676 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 0.58 (26676 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294
• Publications: 0 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADARB2	NM_018702.4	MANE Select	c.100+125977G>C		intron	N/A	NP_061172.1	Q9NS39-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADARB2	ENST00000381312.6	TSL:1 MANE Select	c.100+125977G>C		intron	N/A	ENSP00000370713.1	Q9NS39-1

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88455 AN: 151866 Hom.: 26636 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.583 AC: 88549 AN: 151984 Hom.: 26676 Cov.: 32 AF XY: 0.585 AC XY: 43475 AN XY: 74272

African (AFR) AF: 0.732 AC: 30359 AN: 41462

American (AMR) AF: 0.586 AC: 8947 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2027 AN: 3472

East Asian (EAS) AF: 0.696 AC: 3575 AN: 5136

South Asian (SAS) AF: 0.548 AC: 2630 AN: 4802

European-Finnish (FIN) AF: 0.533 AC: 5624 AN: 10552

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33634 AN: 67984

Other (OTH) AF: 0.588 AC: 1235 AN: 2102

Alfa AF: 0.401 Hom.: 1033

Bravo AF: 0.592

Asia WGS AF: 0.591 AC: 2054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.30
PhyloP100		-0.29
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: rs1874993; hg19: chr10-1653269;