rs2721243

Positions:

• chr8-15800821-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.938-5542C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0671 in 152,122 control chromosomes in the GnomAD database, including 513 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 0.067 (513 hom., cov: 32)
• Consequence: TUSC3 NM_001413679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

Genes affected

TUSC3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TUSC3	NM_001413679.1	c.938-5542C>T		intron_variant			NP_001400608.1
TUSC3	NM_001413684.1	c.1029-5542C>T		intron_variant			NP_001400613.1
TUSC3	NM_001413685.1	c.938-50703C>T		intron_variant			NP_001400614.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0671 AC: 10195 AN: 152004 Hom.: 513 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0427

Gnomad ASJ AF: 0.0900

Gnomad EAS AF: 0.0683

Gnomad SAS AF: 0.0518

Gnomad FIN AF: 0.0214

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0375

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0671 AC: 10210 AN: 152122 Hom.: 513 Cov.: 32 AF XY: 0.0659 AC XY: 4899 AN XY: 74374

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0426

Gnomad4 ASJ AF: 0.0900

Gnomad4 EAS AF: 0.0685

Gnomad4 SAS AF: 0.0527

Gnomad4 FIN AF: 0.0214

Gnomad4 NFE AF: 0.0375

Gnomad4 OTH AF: 0.0652

Alfa AF: 0.0475 Hom.: 90

Bravo AF: 0.0711

Asia WGS AF: 0.0680 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2721243; hg19: chr8-15658330;