rs12415209

Positions:

• chr10-1213439-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.1682+3512G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,084 control chromosomes in the GnomAD database, including 2,013 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 0.15 (2013 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.17

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.1682+3512G>A		intron_variant		ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.1682+3512G>A		intron_variant		1	NM_018702.4	ENSP00000370713	P1
LINC00200	ENST00000655745.1	n.264+52802C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23400 AN: 151966 Hom.: 2011 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.154 AC: 23432 AN: 152084 Hom.: 2013 Cov.: 32 AF XY: 0.158 AC XY: 11744 AN XY: 74348

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.154

Alfa AF: 0.137 Hom.: 348

Bravo AF: 0.161

Asia WGS AF: 0.262 AC: 914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.49

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: rs12415209; hg19: chr10-1259379;