10-1288008-T-C

Position:

• chr10-1288008-T-C

Variant summary

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

The ENST00000381312.6(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 ENST00000381312.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780

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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.1078-16939A>G		intron_variant		ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.1078-16939A>G		intron_variant		1	NM_018702.4	ENSP00000370713	P1
LINC00200	ENST00000655745.1	n.265-465T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.775

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.585

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.84
DANN	Benign	0.51

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: rs1500965; hg19: chr10-1330203;