chr7-47303013-T-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_022748.12(TNS3):c.3394A>T(p.Ile1132Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00119 in 1,613,936 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0019 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 23 hom. )
Consequence
TNS3
NM_022748.12 missense
NM_022748.12 missense
Scores
5
9
5
Clinical Significance
Conservation
PhyloP100: 7.50
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=0.009512037).
BP6
?
Variant 7-47303013-T-A is Benign according to our data. Variant chr7-47303013-T-A is described in ClinVar as [Benign]. Clinvar id is 789514.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 290 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNS3 | NM_022748.12 | c.3394A>T | p.Ile1132Phe | missense_variant | 22/31 | ENST00000311160.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNS3 | ENST00000311160.14 | c.3394A>T | p.Ile1132Phe | missense_variant | 22/31 | 1 | NM_022748.12 |
Frequencies
GnomAD3 genomes ? AF: 0.00191 AC: 290AN: 152202Hom.: 1 Cov.: 33
GnomAD3 genomes
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33
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GnomAD3 exomes AF: 0.00207 AC: 515AN: 249152Hom.: 4 AF XY: 0.00187 AC XY: 253AN XY: 135182
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GnomAD4 exome AF: 0.00111 AC: 1626AN: 1461616Hom.: 23 Cov.: 32 AF XY: 0.00110 AC XY: 803AN XY: 727074
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GnomAD4 genome ? AF: 0.00190 AC: 290AN: 152320Hom.: 1 Cov.: 33 AF XY: 0.00172 AC XY: 128AN XY: 74490
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ESP6500AA
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201
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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 | Invitae | Oct 10, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Pathogenic
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T
MetaSVM
Pathogenic
D
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at