7-47521750-T-G

Variant names:

• chr7-47521750-T-G
• rs334517
• NM_022748.12:c.-153+7286A>C

Variant summary

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

The NM_022748.12(TNS3):​c.-153+7286A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,876 control chromosomes in the GnomAD database, including 9,992 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 0.33 (9992 hom., cov: 31)
• Consequence: TNS3 NM_022748.12 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265

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 (NFE) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNS3	NM_022748.12	c.-153+7286A>C		intron_variant	Intron 2 of 30	ENST00000311160.14	NP_073585.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNS3	ENST00000311160.14	c.-153+7286A>C		intron_variant	Intron 2 of 30	1	NM_022748.12	ENSP00000312143.9

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50851 AN: 151756 Hom.: 9990 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.335 AC: 50843 AN: 151876 Hom.: 9992 Cov.: 31 AF XY: 0.333 AC XY: 24680 AN XY: 74206

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.338

Alfa AF: 0.292 Hom.: 1154

Bravo AF: 0.326

Asia WGS AF: 0.275 AC: 957 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	1.4
DANN	Benign	0.71

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: rs334517; hg19: chr7-47561348;