chr3-120781218-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_005513.3(GTF2E1):c.1068C>T(p.Ser356=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0126 in 1,614,104 control chromosomes in the GnomAD database, including 141 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0094 ( 3 hom., cov: 32)
Exomes 𝑓: 0.013 ( 138 hom. )
Consequence
GTF2E1
NM_005513.3 synonymous
NM_005513.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.271
Genes affected
GTF2E1 (HGNC:4650): (general transcription factor IIE subunit 1) Enables RNA polymerase II general transcription initiation factor activity. Involved in transcription by RNA polymerase II. Located in cytosol and nucleoplasm. Part of transcription factor TFIID complex and transcription preinitiation 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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.31).
BP6
?
Variant 3-120781218-C-T is Benign according to our data. Variant chr3-120781218-C-T is described in ClinVar as [Benign]. Clinvar id is 789165.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.271 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0129 (18861/1461824) while in subpopulation MID AF= 0.0371 (214/5768). AF 95% confidence interval is 0.033. There are 138 homozygotes in gnomad4_exome. There are 9279 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1441 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GTF2E1 | NM_005513.3 | c.1068C>T | p.Ser356= | synonymous_variant | 5/5 | ENST00000283875.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GTF2E1 | ENST00000283875.6 | c.1068C>T | p.Ser356= | synonymous_variant | 5/5 | 1 | NM_005513.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00947 AC: 1441AN: 152160Hom.: 3 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
1441
AN:
152160
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: 0.00932 AC: 2337AN: 250884Hom.: 21 AF XY: 0.00946 AC XY: 1283AN XY: 135560
GnomAD3 exomes
AF:
AC:
2337
AN:
250884
Hom.:
AF XY:
AC XY:
1283
AN XY:
135560
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: 0.0129 AC: 18861AN: 1461824Hom.: 138 Cov.: 32 AF XY: 0.0128 AC XY: 9279AN XY: 727214
GnomAD4 exome
AF:
AC:
18861
AN:
1461824
Hom.:
Cov.:
32
AF XY:
AC XY:
9279
AN XY:
727214
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: 0.00945 AC: 1439AN: 152280Hom.: 3 Cov.: 32 AF XY: 0.00848 AC XY: 631AN XY: 74444
GnomAD4 genome
?
AF:
AC:
1439
AN:
152280
Hom.:
Cov.:
32
AF XY:
AC XY:
631
AN XY:
74444
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:
14
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 | Aug 23, 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