chr10-133230298-C-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_003577.3(UTF1):c.10C>A(p.Arg4=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.845 in 1,069,632 control chromosomes in the GnomAD database, including 384,570 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.77 ( 45012 hom., cov: 31)
Exomes 𝑓: 0.86 ( 339558 hom. )
Consequence
UTF1
NM_003577.3 synonymous
NM_003577.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.569
Genes affected
UTF1 (HGNC:12634): (undifferentiated embryonic cell transcription factor 1) The protein encoded by this gene is a leucine zipper-containing transcriptional coactivator that may link the upstream activator ATF2 with the basal transcription complex. The encoded protein is closely associated with chromatin and is required for the proper differentiation of embryonic carcinoma and embryonic stem cells. Found nearly exclusively in pluripotent cells, this protein can also serve as a transcriptional repressor. [provided by RefSeq, Nov 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
?
Variant 10-133230298-C-A is Benign according to our data. Variant chr10-133230298-C-A is described in ClinVar as [Benign]. Clinvar id is 2787236.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.569 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UTF1 | NM_003577.3 | c.10C>A | p.Arg4= | synonymous_variant | 1/2 | ENST00000304477.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UTF1 | ENST00000304477.3 | c.10C>A | p.Arg4= | synonymous_variant | 1/2 | 1 | NM_003577.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.768 AC: 114359AN: 148960Hom.: 44975 Cov.: 31
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GnomAD4 exome AF: 0.858 AC: 789540AN: 920564Hom.: 339558 Cov.: 41 AF XY: 0.859 AC XY: 371435AN XY: 432550
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GnomAD4 genome ? AF: 0.768 AC: 114447AN: 149068Hom.: 45012 Cov.: 31 AF XY: 0.769 AC XY: 55901AN XY: 72738
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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 | Jan 12, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at