chr8-15452309-A-G

Variant summary

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

The NM_001413670.1(TUSC3):​c.78+29389A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0834 in 152,266 control chromosomes in the GnomAD database, including 749 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 0.083 ( 749 hom., cov: 33)

Consequence

TUSC3
NM_001413670.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.64
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=-0.71).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TUSC3NM_001413670.1 linkuse as main transcriptc.78+29389A>G intron_variant NP_001400599.1
TUSC3NM_001413671.1 linkuse as main transcriptc.-31+35004A>G intron_variant NP_001400600.1
TUSC3NM_001413669.1 linkuse as main transcriptc.-31+35004A>G intron_variant NP_001400598.1
TUSC3NM_001413672.1 linkuse as main transcriptc.-128-31077A>G intron_variant NP_001400601.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TUSC3ENST00000503191.5 linkuse as main transcriptn.92-31077A>G intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.0834
AC:
12693
AN:
152148
Hom.:
749
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.164
Gnomad AMI
AF:
0.0987
Gnomad AMR
AF:
0.0719
Gnomad ASJ
AF:
0.0983
Gnomad EAS
AF:
0.00347
Gnomad SAS
AF:
0.148
Gnomad FIN
AF:
0.0267
Gnomad MID
AF:
0.114
Gnomad NFE
AF:
0.0465
Gnomad OTH
AF:
0.0833
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0834
AC:
12706
AN:
152266
Hom.:
749
Cov.:
33
AF XY:
0.0829
AC XY:
6172
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.164
Gnomad4 AMR
AF:
0.0718
Gnomad4 ASJ
AF:
0.0983
Gnomad4 EAS
AF:
0.00348
Gnomad4 SAS
AF:
0.146
Gnomad4 FIN
AF:
0.0267
Gnomad4 NFE
AF:
0.0465
Gnomad4 OTH
AF:
0.0824
Alfa
AF:
0.0628
Hom.:
116
Bravo
AF:
0.0905
Asia WGS
AF:
0.0830
AC:
289
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.71
CADD
Benign
12
DANN
Benign
0.92

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.

Other links and lift over

dbSNP: rs7833963; hg19: chr8-15309818; API