rs10094375

Positions:

• chr8-15621415-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006765.4(TUSC3):​c.139-1665C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.841 in 149,996 control chromosomes in the GnomAD database, including 53,296 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 0.84 (53296 hom., cov: 29)
• Consequence: TUSC3 NM_006765.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TUSC3	NM_006765.4	c.139-1665C>T		intron_variant		ENST00000503731.6	NP_006756.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TUSC3	ENST00000503731.6	c.139-1665C>T		intron_variant		1	NM_006765.4	ENSP00000424544	A1

Frequencies

GnomAD3 genomes AF: 0.841 AC: 126103 AN: 149938 Hom.: 53264 Cov.: 29

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.768

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.841 AC: 126169 AN: 149996 Hom.: 53296 Cov.: 29 AF XY: 0.839 AC XY: 61431 AN XY: 73230

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.780

Gnomad4 ASJ AF: 0.855

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.931

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.826

Alfa AF: 0.853 Hom.: 9352

Bravo AF: 0.833

Asia WGS AF: 0.764 AC: 2621 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.4
DANN	Benign	0.35

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

Other links and lift over

dbSNP: rs10094375; hg19: chr8-15478924;