chr5-146459281-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBS1BS2
The NM_001382548.1(TCERG1):c.836C>T(p.Pro279Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00141 in 1,614,258 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0073 ( 5 hom., cov: 33)
Exomes 𝑓: 0.00079 ( 20 hom. )
Consequence
TCERG1
NM_001382548.1 missense
NM_001382548.1 missense
Scores
4
14
Clinical Significance
Conservation
PhyloP100: 1.59
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 Benign. Variant got -13 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, TCERG1
BP4
?
Computational evidence support a benign effect (MetaRNN=0.004166484).
BP6
?
Variant 5-146459281-C-T is Benign according to our data. Variant chr5-146459281-C-T is described in ClinVar as [Benign]. Clinvar id is 714282.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0073 (1112/152370) while in subpopulation AFR AF= 0.0251 (1045/41588). AF 95% confidence interval is 0.0239. There are 5 homozygotes in gnomad4. There are 530 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1111 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCERG1 | NM_001382548.1 | c.836C>T | p.Pro279Leu | missense_variant | 4/23 | ENST00000679501.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCERG1 | ENST00000679501.2 | c.836C>T | p.Pro279Leu | missense_variant | 4/23 | NM_001382548.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00730 AC: 1111AN: 152252Hom.: 5 Cov.: 33
GnomAD3 genomes
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1111
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33
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GnomAD3 exomes AF: 0.00196 AC: 492AN: 251454Hom.: 6 AF XY: 0.00135 AC XY: 183AN XY: 135890
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GnomAD4 exome AF: 0.000793 AC: 1160AN: 1461888Hom.: 20 Cov.: 33 AF XY: 0.000652 AC XY: 474AN XY: 727246
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GnomAD4 genome ? AF: 0.00730 AC: 1112AN: 152370Hom.: 5 Cov.: 33 AF XY: 0.00711 AC XY: 530AN XY: 74522
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ESP6500AA
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111
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293
Asia WGS
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5
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3478
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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 | Apr 04, 2018 | - - |
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;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