chr9-79720246-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_007005.6(TLE4):c.1791C>T(p.Ser597=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000594 in 1,614,086 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0022 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00042 ( 4 hom. )
Consequence
TLE4
NM_007005.6 synonymous
NM_007005.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.96
Genes affected
TLE4 (HGNC:11840): (TLE family member 4, transcriptional corepressor) Predicted to enable transcription corepressor activity. Predicted to be involved in negative regulation of canonical Wnt signaling pathway. Predicted to act upstream of or within Wnt signaling pathway; cellular response to leukemia inhibitory factor; and negative regulation of transcription by RNA polymerase II. Located in nucleoplasm. Part of beta-catenin-TCF complex. [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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
?
Variant 9-79720246-C-T is Benign according to our data. Variant chr9-79720246-C-T is described in ClinVar as [Benign]. Clinvar id is 716982.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.96 with no splicing effect.
BS2
?
High AC in GnomAd at 334 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLE4 | NM_007005.6 | c.1791C>T | p.Ser597= | synonymous_variant | 16/20 | ENST00000376552.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLE4 | ENST00000376552.8 | c.1791C>T | p.Ser597= | synonymous_variant | 16/20 | 1 | NM_007005.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00220 AC: 334AN: 152124Hom.: 1 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
334
AN:
152124
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:
GnomAD3 exomes AF: 0.000967 AC: 243AN: 251390Hom.: 0 AF XY: 0.000957 AC XY: 130AN XY: 135862
GnomAD3 exomes
AF:
AC:
243
AN:
251390
Hom.:
AF XY:
AC XY:
130
AN XY:
135862
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000422 AC: 617AN: 1461844Hom.: 4 Cov.: 31 AF XY: 0.000421 AC XY: 306AN XY: 727224
GnomAD4 exome
AF:
AC:
617
AN:
1461844
Hom.:
Cov.:
31
AF XY:
AC XY:
306
AN XY:
727224
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: 0.00225 AC: 342AN: 152242Hom.: 2 Cov.: 32 AF XY: 0.00224 AC XY: 167AN XY: 74430
GnomAD4 genome
?
AF:
AC:
342
AN:
152242
Hom.:
Cov.:
32
AF XY:
AC XY:
167
AN XY:
74430
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:
6
AN:
3478
EpiCase
AF:
EpiControl
AF:
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 | Jun 12, 2018 | - - |
Computational 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