10-1218457-A-T

Variant names:

• chr10-1218457-A-T
• rs12770636
• NM_018702.4:c.1514-1338T>A

Variant summary

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

The NM_018702.4(ADARB2):​c.1514-1338T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,254 control chromosomes in the GnomAD database, including 7,140 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 0.28 (7140 hom., cov: 33)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.1514-1338T>A		intron_variant	Intron 6 of 9	ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.1514-1338T>A		intron_variant	Intron 6 of 9	1	NM_018702.4	ENSP00000370713.1
ADARB2	ENST00000469464.1	n.298-1338T>A		intron_variant	Intron 2 of 2	2
LINC00200	ENST00000655745.1	n.264+57820A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42262 AN: 152136 Hom.: 7139 Cov.: 33

Gnomad AFR AF: 0.0753

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.278 AC: 42258 AN: 152254 Hom.: 7140 Cov.: 33 AF XY: 0.279 AC XY: 20805 AN XY: 74446

African (AFR) AF: 0.0752 AC: 3125 AN: 41574

American (AMR) AF: 0.258 AC: 3953 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1062 AN: 3468

East Asian (EAS) AF: 0.434 AC: 2247 AN: 5180

South Asian (SAS) AF: 0.452 AC: 2182 AN: 4828

European-Finnish (FIN) AF: 0.347 AC: 3666 AN: 10576

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.368 AC: 25059 AN: 68016

Other (OTH) AF: 0.311 AC: 657 AN: 2114

Alfa AF: 0.236 Hom.: 718

Bravo AF: 0.259

Asia WGS AF: 0.429 AC: 1493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.44
PhyloP100		-0.61
Mutation Taster		=99/1	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: rs12770636; hg19: chr10-1264397;