chr7-47539433-C-G
Position:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022748.12(TNS3):c.-264-10286G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 315,550 control chromosomes in the GnomAD database, including 18,232 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 0.30 ( 7939 hom., cov: 33)
Exomes 𝑓: 0.36 ( 10293 hom. )
Consequence
TNS3
NM_022748.12 intron
NM_022748.12 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.63
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNS3 | NM_022748.12 | c.-264-10286G>C | intron_variant | ENST00000311160.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNS3 | ENST00000311160.14 | c.-264-10286G>C | intron_variant | 1 | NM_022748.12 | ||||
TNS3 | ENST00000442536.6 | c.-265+66G>C | intron_variant, NMD_transcript_variant | 1 | |||||
TNS3 | ENST00000434451.1 | c.85-10286G>C | intron_variant | 5 | |||||
TNS3 | ENST00000457718.6 | c.46-10286G>C | intron_variant | 5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.305 AC: 46343AN: 152026Hom.: 7939 Cov.: 33
GnomAD3 genomes
AF:
AC:
46343
AN:
152026
Hom.:
Cov.:
33
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:
GnomAD4 exome AF: 0.355 AC: 58014AN: 163406Hom.: 10293 Cov.: 0 AF XY: 0.355 AC XY: 31157AN XY: 87810
GnomAD4 exome
AF:
AC:
58014
AN:
163406
Hom.:
Cov.:
0
AF XY:
AC XY:
31157
AN XY:
87810
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.305 AC: 46344AN: 152144Hom.: 7939 Cov.: 33 AF XY: 0.306 AC XY: 22735AN XY: 74366
GnomAD4 genome
AF:
AC:
46344
AN:
152144
Hom.:
Cov.:
33
AF XY:
AC XY:
22735
AN XY:
74366
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1228
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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