Variant 8-15787531-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001413679.1(TUSC3):c.938-18832A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0392 in 152,280 control chromosomes in the GnomAD database, including 142 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 0.039 ( 142 hom., cov: 32)

Consequence

TUSC3
NM_001413679.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.28

Variant links:

Genes affected

TUSC3 (HGNC:30242): (tumor suppressor candidate 3) This gene encodes a protein that has been associated with several biological functions including cellular magnesium uptake, protein glycosylation and embryonic development. This protein localizes to the endoplasmic reticulum and acts as a component of the oligosaccharyl transferase complex which is responsible for N-linked protein glycosylation. This gene is a candidate tumor suppressor gene. Homozygous mutations in this gene are associated with autosomal recessive nonsyndromic mental retardation-7 and in the proliferation and invasiveness of several cancers including metastatic pancreatic cancer, ovarian cancer and glioblastoma multiform. [provided by RefSeq, Oct 2017]

TUSC3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein
TUSC3	NM_001413679.1 link	c.938-18832A>T	intron_variant	NP_001400608.1
TUSC3	NM_001413684.1 link	c.1029-18832A>T	intron_variant	NP_001400613.1
TUSC3	NM_001413685.1 link	c.937+43919A>T	intron_variant	NP_001400614.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.0391

AC:

5945

AN:

152162

Hom.:

141

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0721

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0290

Gnomad ASJ

AF:

0.0625

Gnomad EAS

AF:

0.0371

Gnomad SAS

AF:

0.0288

Gnomad FIN

AF:

0.0132

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0253

Gnomad OTH

AF:

0.0439

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

GnomAD4 genome

AF:

0.0392

AC:

5963

AN:

152280

Hom.:

142

Cov.:

AF XY:

0.0389

AC XY:

2896

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.0723

Gnomad4 AMR

AF:

0.0290

Gnomad4 ASJ

AF:

0.0625

Gnomad4 EAS

AF:

0.0370

Gnomad4 SAS

AF:

0.0294

Gnomad4 FIN

AF:

0.0132

Gnomad4 NFE

AF:

0.0253

Gnomad4 OTH

AF:

0.0435

Alfa

AF:

0.00465

Hom.:

Bravo

AF:

0.0415

Asia WGS

AF:

0.0410

AC:

143

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.0090

DANN

Benign

0.80

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over