chr8-15802120-G-A

Variant summary

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

The NM_001413679.1(TUSC3):​c.938-4243G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,068 control chromosomes in the GnomAD database, including 49,349 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 0.81 ( 49349 hom., cov: 31)

Consequence

TUSC3
NM_001413679.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.52
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TUSC3NM_001413679.1 linkuse as main transcriptc.938-4243G>A intron_variant NP_001400608.1
TUSC3NM_001413684.1 linkuse as main transcriptc.1029-4243G>A intron_variant NP_001400613.1
TUSC3NM_001413685.1 linkuse as main transcriptc.938-49404G>A intron_variant NP_001400614.1

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.805
AC:
122344
AN:
151950
Hom.:
49296
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.772
Gnomad AMI
AF:
0.759
Gnomad AMR
AF:
0.803
Gnomad ASJ
AF:
0.821
Gnomad EAS
AF:
0.842
Gnomad SAS
AF:
0.812
Gnomad FIN
AF:
0.769
Gnomad MID
AF:
0.783
Gnomad NFE
AF:
0.828
Gnomad OTH
AF:
0.818
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.805
AC:
122455
AN:
152068
Hom.:
49349
Cov.:
31
AF XY:
0.804
AC XY:
59717
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.772
Gnomad4 AMR
AF:
0.804
Gnomad4 ASJ
AF:
0.821
Gnomad4 EAS
AF:
0.842
Gnomad4 SAS
AF:
0.813
Gnomad4 FIN
AF:
0.769
Gnomad4 NFE
AF:
0.827
Gnomad4 OTH
AF:
0.820
Alfa
AF:
0.800
Hom.:
4721
Bravo
AF:
0.805
Asia WGS
AF:
0.815
AC:
2836
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.0050
DANN
Benign
0.65

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: rs6530906; hg19: chr8-15659629; API