10-1559304-A-G

Variant names:

• chr10-1559304-A-G
• rs2676739
• NM_018702.4:c.100+177747T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018702.4(ADARB2):​c.100+177747T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 152,078 control chromosomes in the GnomAD database, including 25,335 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 (25335 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.100+177747T>C		intron_variant	Intron 1 of 9	ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.100+177747T>C		intron_variant	Intron 1 of 9	1	NM_018702.4	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87153 AN: 151960 Hom.: 25313 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.574 AC: 87219 AN: 152078 Hom.: 25335 Cov.: 32 AF XY: 0.573 AC XY: 42579 AN XY: 74310

African (AFR) AF: 0.545 AC: 22628 AN: 41490

American (AMR) AF: 0.626 AC: 9560 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1918 AN: 3466

East Asian (EAS) AF: 0.750 AC: 3875 AN: 5168

South Asian (SAS) AF: 0.544 AC: 2621 AN: 4820

European-Finnish (FIN) AF: 0.551 AC: 5825 AN: 10576

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38933 AN: 67960

Other (OTH) AF: 0.542 AC: 1144 AN: 2112

Alfa AF: 0.521 Hom.: 3349

Bravo AF: 0.582

Asia WGS AF: 0.638 AC: 2213 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	0.045
DANN	Benign	0.42
PhyloP100		-2.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2676739; hg19: chr10-1601499; COSMIC: COSV67225768; COSMIC: COSV67225768;