rs6530906

Positions:

• chr8-15802120-G-A
• chr8-15802120-G-T

Variant summary

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

The NM_001413679.1(TUSC3):​c.938-4243G>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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

Genes affected

TUSC3 (HGNC:):

ACMG classification

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	UniProt
TUSC3	NM_001413679.1	c.938-4243G>A		intron_variant
TUSC3	NM_001413684.1	c.1029-4243G>A		intron_variant
TUSC3	NM_001413685.1	c.938-49404G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122344 AN: 151950 Hom.: 49296 Cov.: 31

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

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

Other links and lift over

dbSNP: rs6530906; hg19: chr8-15659629;