rs10081561

Variant summary

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

The NM_006765.4(TUSC3):​c.309-10875G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 145,982 control chromosomes in the GnomAD database, including 22,103 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 0.55 ( 22103 hom., cov: 26)

Consequence

TUSC3
NM_006765.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20
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]

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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=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TUSC3NM_006765.4 linkc.309-10875G>A intron_variant Intron 2 of 10 ENST00000503731.6 NP_006756.2 Q13454-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TUSC3ENST00000503731.6 linkc.309-10875G>A intron_variant Intron 2 of 10 1 NM_006765.4 ENSP00000424544.1 Q13454-1

Frequencies

GnomAD3 genomes
AF:
0.552
AC:
80491
AN:
145914
Hom.:
22084
Cov.:
26
show subpopulations
Gnomad AFR
AF:
0.462
Gnomad AMI
AF:
0.564
Gnomad AMR
AF:
0.557
Gnomad ASJ
AF:
0.559
Gnomad EAS
AF:
0.633
Gnomad SAS
AF:
0.512
Gnomad FIN
AF:
0.668
Gnomad MID
AF:
0.560
Gnomad NFE
AF:
0.584
Gnomad OTH
AF:
0.532
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.552
AC:
80537
AN:
145982
Hom.:
22103
Cov.:
26
AF XY:
0.554
AC XY:
39231
AN XY:
70838
show subpopulations
Gnomad4 AFR
AF:
0.462
Gnomad4 AMR
AF:
0.557
Gnomad4 ASJ
AF:
0.559
Gnomad4 EAS
AF:
0.634
Gnomad4 SAS
AF:
0.511
Gnomad4 FIN
AF:
0.668
Gnomad4 NFE
AF:
0.584
Gnomad4 OTH
AF:
0.537
Alfa
AF:
0.559
Hom.:
30261
Bravo
AF:
0.535
Asia WGS
AF:
0.560
AC:
1942
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.11
DANN
Benign
0.40

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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.

Other links and lift over

dbSNP: rs10081561; hg19: chr8-15497331; API