Genetic Variant STUB1-DT:n.17G>A (chr16-679831-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000567091.2(STUB1-DT):n.17G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 145,232 control chromosomes in the GnomAD database, including 12,607 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.41 ( 12597 hom., cov: 25)

Exomes 𝑓: 0.42 ( 10 hom. )

Consequence

STUB1-DT
ENST00000567091.2 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.399

Publications

3 publications found

Variant links:

Genes affected

STUB1-DT (HGNC:54519): (STUB1 divergent transcript)

STUB1-DT links:

ENSG00000294321 (HGNC:):

ENSG00000294321 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 16-679831-C-T is Benign according to our data. Variant chr16-679831-C-T is described in ClinVar as Benign. ClinVar VariationId is 1231549.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STUB1-DT	NR_136337.1 link	n.-54G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
STUB1-DT	ENST00000567091.2 link	n.17G>A	non_coding_transcript_exon_variant	Exon 1 of 4	3
STUB1-DT	ENST00000722589.1 link	n.1G>A	non_coding_transcript_exon_variant	Exon 1 of 4
STUB1-DT	ENST00000722590.1 link	n.1G>A	non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.411

AC:

59621

AN:

145056

Hom.:

12585

Cov.:

show subpopulations

Gnomad AFR

AF:

0.380

Gnomad AMI

AF:

0.360

Gnomad AMR

AF:

0.453

Gnomad ASJ

AF:

0.331

Gnomad EAS

AF:

0.719

Gnomad SAS

AF:

0.682

Gnomad FIN

AF:

0.462

Gnomad MID

AF:

0.311

Gnomad NFE

AF:

0.378

Gnomad OTH

AF:

0.364

GnomAD4 exome

AF:

0.420

AC:

AN:

Hom.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.650

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.175

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.537

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.411

AC:

59657

AN:

145144

Hom.:

12597

Cov.:

AF XY:

0.421

AC XY:

29742

AN XY:

70590

show subpopulations

African (AFR)

AF:

0.380

AC:

14895

AN:

39224

American (AMR)

AF:

0.454

AC:

6664

AN:

14684

Ashkenazi Jewish (ASJ)

AF:

0.331

AC:

1123

AN:

3390

East Asian (EAS)

AF:

0.719

AC:

3433

AN:

4778

South Asian (SAS)

AF:

0.683

AC:

3068

AN:

4492

European-Finnish (FIN)

AF:

0.462

AC:

4377

AN:

9468

Middle Eastern (MID)

AF:

0.304

AC:

AN:

280

European-Non Finnish (NFE)

AF:

0.378

AC:

24950

AN:

65938

Other (OTH)

AF:

0.371

AC:

747

AN:

2016

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.455

Heterozygous variant carriers

1547

3094

4642

6189

7736

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

568

1136

1704

2272

2840

<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:

0.244

Hom.:

577

Bravo

AF:

0.399

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Sep 25, 2019

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

5.3

(source)

DANN

Benign

0.73

PhyloP100

-0.40

PromoterAI

-0.023

Neutral

(source)

Mutation Taster

=100/0

polymorphism

(source)

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over