10-1288008-T-C

Variant names:

• chr10-1288008-T-C
• rs1500965
• NM_018702.4:c.1078-16939A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018702.4(ADARB2):​c.1078-16939A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,178 control chromosomes in the GnomAD database, including 25,033 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 0.57 (25033 hom., cov: 34)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780
• 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]

LINC00200 (HGNC:30974): (long intergenic non-protein coding RNA 200)

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 (SAS) allele frequency at 95% confidence interval = 0.754 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.1078-16939A>G		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.1078-16939A>G		intron	N/A	ENSP00000370713.1
	LINC00200	ENST00000655745.1		n.265-465T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86590 AN: 152060 Hom.: 24991 Cov.: 34

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.570 AC: 86695 AN: 152178 Hom.: 25033 Cov.: 34 AF XY: 0.573 AC XY: 42625 AN XY: 74402

African (AFR) AF: 0.585 AC: 24276 AN: 41512

American (AMR) AF: 0.628 AC: 9617 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1719 AN: 3472

East Asian (EAS) AF: 0.664 AC: 3422 AN: 5150

South Asian (SAS) AF: 0.775 AC: 3739 AN: 4824

European-Finnish (FIN) AF: 0.482 AC: 5112 AN: 10596

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36916 AN: 68000

Other (OTH) AF: 0.585 AC: 1236 AN: 2112

Alfa AF: 0.350 Hom.: 755

Bravo AF: 0.574

Asia WGS AF: 0.740 AC: 2574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.84
DANN	Benign	0.51
PhyloP100		-0.78
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: rs1500965; hg19: chr10-1330203;