dbSNP rs11869222: TOB1-AS1:n.572-631T>C (chr17-50916519-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.290

Publications

1 publications found

Variant links:

Genes affected

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

TOB1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
TOB1-AS1	ENST00000803431.1 link	n.572-631T>C	intron_variant	Intron 3 of 5
TOB1-AS1	ENST00000803432.1 link	n.794-631T>C	intron_variant	Intron 2 of 4
TOB1-AS1	ENST00000803433.1 link	n.586-631T>C	intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

25890

AN:

151932

Hom.:

3083

Cov.:

show subpopulations

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.:

AF XY:

0.184

AC XY:

13664

AN XY:

74338

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.171

AC:

11608

AN:

67970

Other (OTH)

AF:

0.195

AC:

412

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1048

2095

3143

4190

5238

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

290

580

870

1160

1450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

4.1

(source)

DANN

Benign

0.79

PhyloP100

0.29

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over