rs12673398

Variant names:

• chr7-47401695-G-T
• rs12673398
• NM_022748.12:c.724-781C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TNS3	NM_022748.12	c.724-781C>A		intron_variant	Intron 13 of 30	ENST00000311160.14	NP_073585.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNS3	ENST00000311160.14	c.724-781C>A		intron_variant	Intron 13 of 30	1	NM_022748.12	ENSP00000312143.9

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

African (AFR) AF: 0.0294 AC: 1224 AN: 41592

American (AMR) AF: 0.0248 AC: 379 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0317 AC: 110 AN: 3472

East Asian (EAS) AF: 0.0756 AC: 391 AN: 5174

South Asian (SAS) AF: 0.0464 AC: 224 AN: 4828

European-Finnish (FIN) AF: 0.0564 AC: 599 AN: 10616

Middle Eastern (MID) AF: 0.0411 AC: 12 AN: 292

European-Non Finnish (NFE) AF: 0.0247 AC: 1680 AN: 68036

Other (OTH) AF: 0.0241 AC: 51 AN: 2116

Alfa AF: 0.0300 Hom.: 36

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
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12673398; hg19: chr7-47441292;