rs11869222

Variant names:

• chr17-50916519-T-C
• rs11869222
• ENST00000803431.1:n.572-631T>C

Variant summary

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

The ENST00000803431.1(TOB1-AS1):​n.572-631T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,050 control chromosomes in the GnomAD database, including 3,080 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 0.17 (3080 hom., cov: 32)
• Consequence: TOB1-AS1 ENST00000803431.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290
• Publications: 1 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.397 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TOB1-AS1	ENST00000803431.1		n.572-631T>C		intron	N/A
	TOB1-AS1	ENST00000803432.1		n.794-631T>C		intron	N/A
	TOB1-AS1	ENST00000803433.1		n.586-631T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25890 AN: 151932 Hom.: 3083 Cov.: 32

Gnomad AFR AF: 0.0410

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.170 AC: 25882 AN: 152050 Hom.: 3080 Cov.: 32 AF XY: 0.184 AC XY: 13664 AN XY: 74338

African (AFR) AF: 0.0409 AC: 1696 AN: 41468

American (AMR) AF: 0.264 AC: 4041 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2042 AN: 5156

South Asian (SAS) AF: 0.412 AC: 1985 AN: 4818

European-Finnish (FIN) AF: 0.286 AC: 3022 AN: 10564

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11608 AN: 67970

Other (OTH) AF: 0.195 AC: 412 AN: 2112

Alfa AF: 0.130 Hom.: 677

Bravo AF: 0.159

Asia WGS AF: 0.364 AC: 1267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.79
PhyloP100		0.29

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11869222;

hg19: chr17-48993880;