7-47291996-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_022748.12(TNS3):c.3887C>T(p.Thr1296Met) variant causes a missense change. The variant allele was found at a frequency of 0.00753 in 1,614,146 control chromosomes in the GnomAD database, including 61 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0051 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0078 ( 59 hom. )
Consequence
TNS3
NM_022748.12 missense
NM_022748.12 missense
Scores
13
6
Clinical Significance
Conservation
PhyloP100: 6.97
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.008240819).
BP6
Variant 7-47291996-G-A is Benign according to our data. Variant chr7-47291996-G-A is described in ClinVar as [Benign]. Clinvar id is 770935.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 776 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00510 AC: 776AN: 152196Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.00500 AC: 1246AN: 249358Hom.: 6 AF XY: 0.00498 AC XY: 674AN XY: 135280
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GnomAD4 exome AF: 0.00778 AC: 11376AN: 1461832Hom.: 59 Cov.: 30 AF XY: 0.00760 AC XY: 5529AN XY: 727220
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GnomAD4 genome AF: 0.00509 AC: 776AN: 152314Hom.: 2 Cov.: 33 AF XY: 0.00470 AC XY: 350AN XY: 74476
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41
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69
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at