rs12673398

chr7-47401695-G-T

Variant summary

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

The NM_022748.12(TNS3):c.724-781C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0307 in 152,342 control chromosomes in the GnomAD database, including 88 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 0.031 (88 hom., cov: 33)
• Consequence: TNS3 NM_022748.12 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114

Genes affected

TNS3 (HGNC:21616): (tensin 3) Predicted to enable phosphatase activity. Predicted to be involved in dephosphorylation and intracellular signal transduction. Predicted to act upstream of or within cell migration; lung alveolus development; and positive regulation of cell population proliferation. Located in cytosol and focal adhesion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNS3	NM_022748.12	c.724-781C>A		intron_variant		ENST00000311160.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNS3	ENST00000311160.14	c.724-781C>A		intron_variant		1	NM_022748.12

Frequencies

GnomAD3 genomes AF: 0.0307 AC: 4674 AN: 152224 Hom.: 87 Cov.: 33

Gnomad AFR AF: 0.0295

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0245

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.0756

Gnomad SAS AF: 0.0464

Gnomad FIN AF: 0.0564

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.0247

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0307 AC: 4676 AN: 152342 Hom.: 88 Cov.: 33 AF XY: 0.0320 AC XY: 2386 AN XY: 74492

Gnomad4 AFR AF: 0.0294

Gnomad4 AMR AF: 0.0248

Gnomad4 ASJ AF: 0.0317

Gnomad4 EAS AF: 0.0756

Gnomad4 SAS AF: 0.0464

Gnomad4 FIN AF: 0.0564

Gnomad4 NFE AF: 0.0247

Gnomad4 OTH AF: 0.0241

Alfa AF: 0.0311 Hom.: 22

Bravo AF: 0.0287

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.91
Dann	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12673398; hg19: chr7-47441292;