chr7-47455361-G-A

Position:

• chr7-47455361-G-A

Variant summary

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

The NM_022748.12(TNS3):​c.-75-13306C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,050 control chromosomes in the GnomAD database, including 5,310 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 0.26 (5310 hom., cov: 32)
• Consequence: TNS3 NM_022748.12 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.808

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNS3	NM_022748.12	c.-75-13306C>T		intron_variant		ENST00000311160.14	NP_073585.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNS3	ENST00000311160.14	c.-75-13306C>T		intron_variant		1	NM_022748.12	ENSP00000312143.9

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39876 AN: 151932 Hom.: 5298 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.263 AC: 39920 AN: 152050 Hom.: 5310 Cov.: 32 AF XY: 0.258 AC XY: 19175 AN XY: 74354

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.272

Alfa AF: 0.264 Hom.: 6152

Bravo AF: 0.266

Asia WGS AF: 0.234 AC: 816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.57

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: rs2941528; hg19: chr7-47494959;