NM_001387777.1:c.4954+352C>T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001387777.1(TNS1):c.4954+352C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0723 in 152,166 control chromosomes in the GnomAD database, including 509 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 0.072 ( 509 hom., cov: 32)
Consequence
TNS1
NM_001387777.1 intron
NM_001387777.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.816
Publications
8 publications found
Genes affected
TNS1 (HGNC:11973): (tensin 1) The protein encoded by this gene localizes to focal adhesions, regions of the plasma membrane where the cell attaches to the extracellular matrix. This protein crosslinks actin filaments and contains a Src homology 2 (SH2) domain, which is often found in molecules involved in signal transduction. This protein is a substrate of calpain II. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2015]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNS1 | NM_001387777.1 | c.4954+352C>T | intron_variant | Intron 27 of 32 | ENST00000682258.1 | NP_001374706.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0723 AC: 10993AN: 152048Hom.: 509 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
10993
AN:
152048
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0723 AC: 10995AN: 152166Hom.: 509 Cov.: 32 AF XY: 0.0706 AC XY: 5254AN XY: 74396 show subpopulations
GnomAD4 genome
AF:
AC:
10995
AN:
152166
Hom.:
Cov.:
32
AF XY:
AC XY:
5254
AN XY:
74396
show subpopulations
African (AFR)
AF:
AC:
1441
AN:
41510
American (AMR)
AF:
AC:
791
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
AC:
350
AN:
3468
East Asian (EAS)
AF:
AC:
9
AN:
5158
South Asian (SAS)
AF:
AC:
113
AN:
4824
European-Finnish (FIN)
AF:
AC:
1012
AN:
10604
Middle Eastern (MID)
AF:
AC:
9
AN:
294
European-Non Finnish (NFE)
AF:
AC:
6983
AN:
67990
Other (OTH)
AF:
AC:
139
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.509
Heterozygous variant carriers
0
533
1066
1598
2131
2664
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
130
260
390
520
650
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
97
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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