chr7-47394031-T-C

Variant names:

• chr7-47394031-T-C
• rs2462634
• NM_022748.12:c.1024+2769A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022748.12(TNS3):​c.1024+2769A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 151,878 control chromosomes in the GnomAD database, including 34,855 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 0.68 (34855 hom., cov: 30)
• Consequence: TNS3 NM_022748.12 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 1 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022748.12. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNS3	NM_022748.12	MANE Select	c.1024+2769A>G		intron	N/A	NP_073585.8
	TNS3	NM_001410877.1		c.1366+2769A>G		intron	N/A	NP_001397806.1	A0A994J537
	TNS3	NM_001410878.1		c.1333+2769A>G		intron	N/A	NP_001397807.1	E9PCX8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNS3	ENST00000311160.14	TSL:1 MANE Select	c.1024+2769A>G		intron	N/A	ENSP00000312143.9	Q68CZ2-1
	TNS3	ENST00000705350.1		c.1366+2769A>G		intron	N/A	ENSP00000516118.1	A0A994J537
	TNS3	ENST00000457718.6	TSL:5	c.1333+2769A>G		intron	N/A	ENSP00000414358.2	E9PCX8

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102527 AN: 151760 Hom.: 34816 Cov.: 30

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.676 AC: 102628 AN: 151878 Hom.: 34855 Cov.: 30 AF XY: 0.676 AC XY: 50215 AN XY: 74258

African (AFR) AF: 0.679 AC: 28098 AN: 41394

American (AMR) AF: 0.678 AC: 10354 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2073 AN: 3468

East Asian (EAS) AF: 0.820 AC: 4227 AN: 5156

South Asian (SAS) AF: 0.493 AC: 2367 AN: 4800

European-Finnish (FIN) AF: 0.740 AC: 7813 AN: 10564

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.669 AC: 45454 AN: 67914

Other (OTH) AF: 0.683 AC: 1436 AN: 2104

Alfa AF: 0.674 Hom.: 5569

Bravo AF: 0.673

Asia WGS AF: 0.688 AC: 2393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.2
DANN	Benign	0.59
PhyloP100		-0.49
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: rs2462634; hg19: chr7-47433628;