16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAGCAGCAGCAGCAGCAGCAG
Variant summary
Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP3BP6_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
Publications
11 publications found
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 was made for transcript
Our verdict: Benign. The variant received -7 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001950.4
BP6
Variant 16-67195890-ACAGCAG-A is Benign according to our data. Variant chr16-67195890-ACAGCAG-A is described in ClinVar as Benign. ClinVar VariationId is 2646614.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 399 AD gene.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001950.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| E2F4 | NM_001950.4 | MANE Select | c.953_958delGCAGCA | p.Ser318_Ser319del | disruptive_inframe_deletion | Exon 7 of 10 | NP_001941.2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| E2F4 | ENST00000379378.8 | TSL:1 MANE Select | c.953_958delGCAGCA | p.Ser318_Ser319del | disruptive_inframe_deletion | Exon 7 of 10 | ENSP00000368686.3 | Q16254 | |
| E2F4 | ENST00000914909.1 | c.953_958delGCAGCA | p.Ser318_Ser319del | disruptive_inframe_deletion | Exon 7 of 10 | ENSP00000584968.1 | |||
| E2F4 | ENST00000957228.1 | c.968_973delGCAGCA | p.Ser323_Ser324del | disruptive_inframe_deletion | Exon 7 of 10 | ENSP00000627287.1 |
Frequencies
GnomAD3 genomes 0.00265 AC: 399AN: 150346Hom.: 2 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
399
AN:
150346
Hom.:
Cov.:
31
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:
GnomAD4 exome AF: 0.00266 AC: 3877AN: 1457006Hom.: 2 AF XY: 0.00272 AC XY: 1968AN XY: 724714 show subpopulations
GnomAD4 exome
AF:
AC:
3877
AN:
1457006
Hom.:
AF XY:
AC XY:
1968
AN XY:
724714
show subpopulations
African (AFR)
AF:
AC:
89
AN:
32888
American (AMR)
AF:
AC:
124
AN:
44560
Ashkenazi Jewish (ASJ)
AF:
AC:
14
AN:
26056
East Asian (EAS)
AF:
AC:
35
AN:
39492
South Asian (SAS)
AF:
AC:
305
AN:
85710
European-Finnish (FIN)
AF:
AC:
10
AN:
52970
Middle Eastern (MID)
AF:
AC:
8
AN:
5726
European-Non Finnish (NFE)
AF:
AC:
3112
AN:
1109536
Other (OTH)
AF:
AC:
180
AN:
60068
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.442
Heterozygous variant carriers
0
252
504
757
1009
1261
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
126
252
378
504
630
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.00265 AC: 399AN: 150442Hom.: 2 Cov.: 31 AF XY: 0.00266 AC XY: 195AN XY: 73438 show subpopulations
GnomAD4 genome
AF:
AC:
399
AN:
150442
Hom.:
Cov.:
31
AF XY:
AC XY:
195
AN XY:
73438
show subpopulations
African (AFR)
AF:
AC:
110
AN:
40830
American (AMR)
AF:
AC:
81
AN:
15116
Ashkenazi Jewish (ASJ)
AF:
AC:
3
AN:
3464
East Asian (EAS)
AF:
AC:
5
AN:
5132
South Asian (SAS)
AF:
AC:
17
AN:
4774
European-Finnish (FIN)
AF:
AC:
1
AN:
10258
Middle Eastern (MID)
AF:
AC:
1
AN:
294
European-Non Finnish (NFE)
AF:
AC:
172
AN:
67572
Other (OTH)
AF:
AC:
9
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.489
Heterozygous variant carriers
0
16
32
49
65
81
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
10
20
30
40
50
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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