chr7-47303115-G-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_022748.12(TNS3):c.3292C>G(p.Leu1098Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00651 in 1,614,048 control chromosomes in the GnomAD database, including 66 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0052 ( 3 hom., cov: 33)
Exomes 𝑓: 0.0066 ( 63 hom. )
Consequence
TNS3
NM_022748.12 missense
NM_022748.12 missense
Scores
6
9
3
Clinical Significance
Conservation
PhyloP100: 8.85
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 -16 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.008170128).
BP6
?
Variant 7-47303115-G-C is Benign according to our data. Variant chr7-47303115-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 713684.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High AC in GnomAd at 797 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNS3 | NM_022748.12 | c.3292C>G | p.Leu1098Val | missense_variant | 22/31 | ENST00000311160.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNS3 | ENST00000311160.14 | c.3292C>G | p.Leu1098Val | missense_variant | 22/31 | 1 | NM_022748.12 |
Frequencies
GnomAD3 genomes ? AF: 0.00523 AC: 797AN: 152246Hom.: 3 Cov.: 33
GnomAD3 genomes
?
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797
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33
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GnomAD3 exomes AF: 0.00557 AC: 1382AN: 248274Hom.: 14 AF XY: 0.00576 AC XY: 777AN XY: 134984
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GnomAD4 exome AF: 0.00664 AC: 9710AN: 1461686Hom.: 63 Cov.: 32 AF XY: 0.00653 AC XY: 4751AN XY: 727122
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GnomAD4 genome ? AF: 0.00523 AC: 797AN: 152362Hom.: 3 Cov.: 33 AF XY: 0.00548 AC XY: 408AN XY: 74504
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20
ESP6500AA
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ESP6500EA
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51
ExAC
?
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653
Asia WGS
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3478
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | TNS3: BS2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Pathogenic
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Uncertain
D;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
MetaRNN
Benign
T;T
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
M;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
N;N
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Uncertain
D;.
Polyphen
D;.
Vest4
MVP
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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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