10-1191823-C-T

Position:

• chr10-1191823-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018702.4(ADARB2):​c.1865-6784G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,040 control chromosomes in the GnomAD database, including 5,180 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 0.23 (5180 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADARB2	NM_018702.4	c.1865-6784G>A		intron_variant		ENST00000381312.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADARB2	ENST00000381312.6	c.1865-6784G>A		intron_variant		1	NM_018702.4	P1
LINC00200	ENST00000655745.1	n.264+31186C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34442 AN: 151922 Hom.: 5169 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.227 AC: 34489 AN: 152040 Hom.: 5180 Cov.: 32 AF XY: 0.229 AC XY: 17055 AN XY: 74326

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.197

Alfa AF: 0.178 Hom.: 397

Bravo AF: 0.245

Asia WGS AF: 0.312 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.38

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: rs950628; hg19: chr10-1237763;