5-146463697-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_001382548.1(TCERG1):c.1039T>C(p.Ser347Pro) variant causes a missense change. The variant allele was found at a frequency of 0.0000477 in 1,614,144 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00028 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
TCERG1
NM_001382548.1 missense
NM_001382548.1 missense
Scores
4
15
Clinical Significance
Conservation
PhyloP100: 3.78
Genes affected
TCERG1 (HGNC:15630): (transcription elongation regulator 1) This gene encodes a nuclear protein that regulates transcriptional elongation and pre-mRNA splicing. The encoded protein interacts with the hyperphosphorylated C-terminal domain of RNA polymerase II via multiple FF domains, and with the pre-mRNA splicing factor SF1 via a WW domain. Alternative splicing results in multiple transcripts variants encoding different isoforms. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, TCERG1
BP4
?
Computational evidence support a benign effect (MetaRNN=0.08632997).
BS2
?
High AC in GnomAd at 43 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCERG1 | NM_001382548.1 | c.1039T>C | p.Ser347Pro | missense_variant | 5/23 | ENST00000679501.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCERG1 | ENST00000679501.2 | c.1039T>C | p.Ser347Pro | missense_variant | 5/23 | NM_001382548.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000283 AC: 43AN: 152132Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251490Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135918
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GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461894Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727248
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GnomAD4 genome ? AF: 0.000282 AC: 43AN: 152250Hom.: 0 Cov.: 33 AF XY: 0.000296 AC XY: 22AN XY: 74436
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2021 | The c.1039T>C (p.S347P) alteration is located in exon 5 (coding exon 5) of the TCERG1 gene. This alteration results from a T to C substitution at nucleotide position 1039, causing the serine (S) at amino acid position 347 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MVP
MPC
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