ENST00000803431.1:n.572-239A>G

Variant names:

• chr17-50916911-A-G
• rs8066630
• ENST00000803431.1:n.572-239A>G

Variant summary

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

The ENST00000803431.1(TOB1-AS1):​n.572-239A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,836 control chromosomes in the GnomAD database, including 8,612 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 0.33 (8612 hom., cov: 32)
• Consequence: TOB1-AS1 ENST00000803431.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 2 publications found

Genes affected

TOB1-AS1 (HGNC:44340): (TOB1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803431.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TOB1-AS1	ENST00000803431.1		n.572-239A>G		intron	N/A
	TOB1-AS1	ENST00000803432.1		n.794-239A>G		intron	N/A
	TOB1-AS1	ENST00000803433.1		n.586-239A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49576 AN: 151718 Hom.: 8604 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.327 AC: 49608 AN: 151836 Hom.: 8612 Cov.: 32 AF XY: 0.338 AC XY: 25040 AN XY: 74188

African (AFR) AF: 0.292 AC: 12068 AN: 41342

American (AMR) AF: 0.377 AC: 5753 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1320 AN: 3470

East Asian (EAS) AF: 0.625 AC: 3212 AN: 5142

South Asian (SAS) AF: 0.552 AC: 2663 AN: 4820

European-Finnish (FIN) AF: 0.373 AC: 3928 AN: 10528

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19563 AN: 67948

Other (OTH) AF: 0.361 AC: 761 AN: 2106

Alfa AF: 0.309 Hom.: 14850

Bravo AF: 0.322

Asia WGS AF: 0.579 AC: 2013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.1
DANN	Benign	0.60
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs8066630; hg19: chr17-48994272;