chr7-47455361-G-A

Variant names:

• chr7-47455361-G-A
• rs2941528
• NM_022748.12:c.-75-13306C>T

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.91).
• 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 rank	MANE	Protein	UniProt
TNS3	NM_022748.12	c.-75-13306C>T		intron_variant	Intron 4 of 30	ENST00000311160.14	NP_073585.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNS3	ENST00000311160.14	c.-75-13306C>T		intron_variant	Intron 4 of 30	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

African (AFR) AF: 0.291 AC: 12066 AN: 41424

American (AMR) AF: 0.237 AC: 3621 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 790 AN: 3472

East Asian (EAS) AF: 0.233 AC: 1204 AN: 5168

South Asian (SAS) AF: 0.238 AC: 1149 AN: 4824

European-Finnish (FIN) AF: 0.221 AC: 2336 AN: 10570

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17932 AN: 67990

Other (OTH) AF: 0.272 AC: 575 AN: 2114

Alfa AF: 0.265 Hom.: 8110

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
PhyloP100		0.81
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: rs2941528; hg19: chr7-47494959;