rs16949486

Variant names:

• chr17-50913996-G-A
• rs16949486
• ENST00000803431.1:n.571+2216G>A

Variant summary

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

The ENST00000803431.1(TOB1-AS1):​n.571+2216G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,070 control chromosomes in the GnomAD database, including 2,381 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 (2381 hom., cov: 31)
• Consequence: TOB1-AS1 ENST00000803431.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.393 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TOB1-AS1	ENST00000803431.1		n.571+2216G>A		intron	N/A
	TOB1-AS1	ENST00000803432.1		n.793+2216G>A		intron	N/A
	TOB1-AS1	ENST00000803433.1		n.585+2216G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22254 AN: 151952 Hom.: 2384 Cov.: 31

Gnomad AFR AF: 0.0325

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.146 AC: 22252 AN: 152070 Hom.: 2381 Cov.: 31 AF XY: 0.159 AC XY: 11820 AN XY: 74326

African (AFR) AF: 0.0325 AC: 1346 AN: 41456

American (AMR) AF: 0.200 AC: 3060 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 836 AN: 3468

East Asian (EAS) AF: 0.393 AC: 2027 AN: 5162

South Asian (SAS) AF: 0.408 AC: 1964 AN: 4816

European-Finnish (FIN) AF: 0.250 AC: 2643 AN: 10576

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9874 AN: 67994

Other (OTH) AF: 0.166 AC: 351 AN: 2112

Alfa AF: 0.147 Hom.: 5683

Bravo AF: 0.132

Asia WGS AF: 0.355 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.71
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs16949486; hg19: chr17-48991357;