rs12681567

Positions:

• chr8-15800094-C-A

Variant summary

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

The NM_001413679.1(TUSC3):​c.938-6269C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0998 in 152,216 control chromosomes in the GnomAD database, including 1,099 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 0.10 (1099 hom., cov: 32)
• Consequence: TUSC3 NM_001413679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

Genes affected

TUSC3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TUSC3	NM_001413679.1	c.938-6269C>A		intron_variant			NP_001400608.1
TUSC3	NM_001413684.1	c.1029-6269C>A		intron_variant			NP_001400613.1
TUSC3	NM_001413685.1	c.938-51430C>A		intron_variant			NP_001400614.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0998 AC: 15176 AN: 152098 Hom.: 1090 Cov.: 32

Gnomad AFR AF: 0.0310

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0599

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0998 AC: 15197 AN: 152216 Hom.: 1099 Cov.: 32 AF XY: 0.103 AC XY: 7688 AN XY: 74416

Gnomad4 AFR AF: 0.0309

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.0599

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.117

Alfa AF: 0.111 Hom.: 919

Bravo AF: 0.108

Asia WGS AF: 0.204 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.26
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12681567; hg19: chr8-15657603;