chr10-1489806-TAATAATTAGCATATTAGGATCAAACAC-T

Position:

• chr10-1489806-TAATAATTAGCATATTAGGATCAAACAC-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_018702.4(ADARB2):​c.101-110673_101-110647delGTGTTTGATCCTAATATGCTAATTATT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,210 control chromosomes in the GnomAD database, including 1,680 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (1680 hom., cov: 31)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.885

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.101-110673_101-110647delGTGTTTGATCCTAATATGCTAATTATT		intron_variant		ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.101-110673_101-110647delGTGTTTGATCCTAATATGCTAATTATT		intron_variant		1	NM_018702.4	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16888 AN: 152092 Hom.: 1672 Cov.: 31

Gnomad AFR AF: 0.0245

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0969

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.111 AC: 16911 AN: 152210 Hom.: 1680 Cov.: 31 AF XY: 0.118 AC XY: 8814 AN XY: 74418

Gnomad4 AFR AF: 0.0246

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.0969

Gnomad4 OTH AF: 0.113

Alfa AF: 0.107 Hom.: 122

Bravo AF: 0.124

Asia WGS AF: 0.235 AC: 816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6143734; hg19: chr10-1532001;