rs17293817

chr10-1410591-G-A

Variant summary

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

The NM_018702.4(ADARB2):c.101-31431C>T 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 152,054 control chromosomes in the GnomAD database, including 6,619 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 (6619 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

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]

LOC124902364 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADARB2	NM_018702.4	c.101-31431C>T		intron_variant		ENST00000381312.6
LOC124902364	XR_007062032.1	n.508-135G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADARB2	ENST00000381312.6	c.101-31431C>T		intron_variant		1	NM_018702.4	P1

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42234 AN: 151936 Hom.: 6614 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.278 AC: 42264 AN: 152054 Hom.: 6619 Cov.: 32 AF XY: 0.281 AC XY: 20872 AN XY: 74324

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.289

Alfa AF: 0.332 Hom.: 14513

Bravo AF: 0.262

Asia WGS AF: 0.261 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.56
Dann	Benign	0.56

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: rs17293817; hg19: chr10-1452786;