rs352780

chr8-15783549-C-Gchr8-15783549-C-T

Variant summary

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

The NM_001413679.1(TUSC3):c.938-22814C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 151,780 control chromosomes in the GnomAD database, including 4,105 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 0.22 (4105 hom., cov: 32)
• Consequence: TUSC3 NM_001413679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249

Genes affected

TUSC3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TUSC3	NM_001413679.1	c.938-22814C>G		intron_variant
TUSC3	NM_001413684.1	c.1029-22814C>G		intron_variant
TUSC3	NM_001413685.1	c.937+39937C>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33777 AN: 151664 Hom.: 4084 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.223 AC: 33818 AN: 151780 Hom.: 4105 Cov.: 32 AF XY: 0.222 AC XY: 16499 AN XY: 74182

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.236

Alfa AF: 0.224 Hom.: 504

Bravo AF: 0.237

Asia WGS AF: 0.230 AC: 797 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.0
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs352780; hg19: chr8-15641058; COSMIC: COSV56061300;