16-67195890-ACAGCAG-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001950.4(E2F4):c.953_958delGCAGCA(p.Ser318_Ser319del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00266 in 1,607,448 control chromosomes in the GnomAD database, including 4 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0027 ( 2 hom., cov: 31)
Exomes 𝑓: 0.0027 ( 2 hom. )
Consequence
E2F4
NM_001950.4 disruptive_inframe_deletion
NM_001950.4 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.77
Genes affected
E2F4 (HGNC:3118): (E2F transcription factor 4) The protein encoded by this gene is a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cell cycle and action of tumor suppressor proteins and is also a target of the transforming proteins of small DNA tumor viruses. The E2F proteins contain several evolutionally conserved domains found in most members of the family. These domains include a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. This protein binds to all three of the tumor suppressor proteins pRB, p107 and p130, but with higher affinity to the last two. It plays an important role in the suppression of proliferation-associated genes, and its gene mutation and increased expression may be associated with human cancer. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
Variant 16-67195890-ACAGCAG-A is Benign according to our data. Variant chr16-67195890-ACAGCAG-A is described in ClinVar as [Benign]. Clinvar id is 2646614.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 399 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00265 AC: 399AN: 150346Hom.: 2 Cov.: 31
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GnomAD4 exome AF: 0.00266 AC: 3877AN: 1457006Hom.: 2 AF XY: 0.00272 AC XY: 1968AN XY: 724714
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GnomAD4 genome AF: 0.00265 AC: 399AN: 150442Hom.: 2 Cov.: 31 AF XY: 0.00266 AC XY: 195AN XY: 73438
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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
Feb 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
E2F4: BS1, BS2 -
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at