rs2838810

Positions:

• chr21-45203408-A-G

Variant summary

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

The NM_001112.4(ADARB1):​c.1566-1147A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,082 control chromosomes in the GnomAD database, including 2,284 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 (2284 hom., cov: 33)
• Consequence: ADARB1 NM_001112.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

ADARB1 (HGNC:226): (adenosine deaminase RNA specific B1) This gene encodes the enzyme responsible for pre-mRNA editing of the glutamate receptor subunit B by site-specific deamination of adenosines. Studies in rat found that this enzyme acted on its own pre-mRNA molecules to convert an AA dinucleotide to an AI dinucleotide which resulted in a new splice site. Alternative splicing of this gene results in several transcript variants, some of which have been characterized by the presence or absence of an ALU cassette insert and a short or long C-terminal region. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADARB1	NM_001112.4	c.1566-1147A>G		intron_variant		ENST00000348831.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADARB1	ENST00000348831.9	c.1566-1147A>G		intron_variant		1	NM_001112.4	P1

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22449 AN: 151964 Hom.: 2274 Cov.: 33

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.0687

Gnomad FIN AF: 0.0777

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0799

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.148 AC: 22510 AN: 152082 Hom.: 2284 Cov.: 33 AF XY: 0.147 AC XY: 10916 AN XY: 74354

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.0684

Gnomad4 FIN AF: 0.0777

Gnomad4 NFE AF: 0.0800

Gnomad4 OTH AF: 0.153

Alfa AF: 0.0988 Hom.: 506

Bravo AF: 0.162

Asia WGS AF: 0.104 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.42
DANN	Benign	0.73

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: rs2838810; hg19: chr21-46623323;