rs7073579

Variant names:

• chr10-1331812-G-A
• rs7073579
• NM_018702.4:c.1077+31216C>T

Variant summary

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

The NM_018702.4(ADARB2):​c.1077+31216C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,978 control chromosomes in the GnomAD database, including 16,609 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 0.46 (16609 hom., cov: 32)
• Consequence: ADARB2 NM_018702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.520
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADARB2	NM_018702.4	c.1077+31216C>T		intron_variant	Intron 3 of 9	ENST00000381312.6	NP_061172.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADARB2	ENST00000381312.6	c.1077+31216C>T		intron_variant	Intron 3 of 9	1	NM_018702.4	ENSP00000370713.1

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69739 AN: 151860 Hom.: 16567 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.460 AC: 69835 AN: 151978 Hom.: 16609 Cov.: 32 AF XY: 0.455 AC XY: 33781 AN XY: 74288

African (AFR) AF: 0.592 AC: 24549 AN: 41434

American (AMR) AF: 0.380 AC: 5805 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1637 AN: 3468

East Asian (EAS) AF: 0.299 AC: 1551 AN: 5182

South Asian (SAS) AF: 0.344 AC: 1658 AN: 4818

European-Finnish (FIN) AF: 0.391 AC: 4123 AN: 10532

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.428 AC: 29086 AN: 67952

Other (OTH) AF: 0.468 AC: 989 AN: 2112

Alfa AF: 0.436 Hom.: 18294

Bravo AF: 0.464

Asia WGS AF: 0.336 AC: 1172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.074
DANN	Benign	0.54
PhyloP100		-0.52
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: rs7073579; hg19: chr10-1374007;