rs3830472
Variant names:
Your query was ambiguous. Multiple possible variants found:
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-A
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAG
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAG
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAGCAG
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAGCAGCAG
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAGCAGCAGCAG
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAGCAGCAGCAGCAG
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAGCAGCAGCAGCAGCAG
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAGCAGCAGCAGCAGCAGCAG
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAGCAGCAGCAGCAGCAGCAGCAG
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG
- chr16-67195890-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAG-ACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP3BS2
The NM_001950.4(E2F4):c.929_958delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA(p.Ser310_Ser319del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00000995 in 1,608,080 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000096 ( 0 hom. )
Consequence
E2F4
NM_001950.4 disruptive_inframe_deletion
NM_001950.4 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
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: Likely_benign. The variant received -5 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001950.4
BS2
High AC in GnomAdExome4 at 14 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.929_958delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA | p.Ser310_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.929_958delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA | p.Ser310_Ser319del | disruptive_inframe_deletion | Exon 7 of 10 | ENSP00000368686.3 | Q16254 | |
| E2F4 | ENST00000914909.1 | c.929_958delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA | p.Ser310_Ser319del | disruptive_inframe_deletion | Exon 7 of 10 | ENSP00000584968.1 | |||
| E2F4 | ENST00000957228.1 | c.944_973delGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA | p.Ser315_Ser324del | disruptive_inframe_deletion | Exon 7 of 10 | ENSP00000627287.1 |
Frequencies
GnomAD3 genomes 0.0000133 AC: 2AN: 150350Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
150350
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: 0.00000960 AC: 14AN: 1457634Hom.: 0 AF XY: 0.00000828 AC XY: 6AN XY: 725044 show subpopulations
GnomAD4 exome
AF:
AC:
14
AN:
1457634
Hom.:
AF XY:
AC XY:
6
AN XY:
725044
show subpopulations
African (AFR)
AF:
AC:
1
AN:
32892
American (AMR)
AF:
AC:
1
AN:
44574
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
26076
East Asian (EAS)
AF:
AC:
0
AN:
39534
South Asian (SAS)
AF:
AC:
0
AN:
85730
European-Finnish (FIN)
AF:
AC:
0
AN:
53052
Middle Eastern (MID)
AF:
AC:
0
AN:
5730
European-Non Finnish (NFE)
AF:
AC:
11
AN:
1109940
Other (OTH)
AF:
AC:
0
AN:
60106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.486
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
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>80
Age
GnomAD4 genome 0.0000133 AC: 2AN: 150446Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73442 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
150446
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
73442
show subpopulations
African (AFR)
AF:
AC:
1
AN:
40830
American (AMR)
AF:
AC:
0
AN:
15118
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3464
East Asian (EAS)
AF:
AC:
0
AN:
5132
South Asian (SAS)
AF:
AC:
0
AN:
4774
European-Finnish (FIN)
AF:
AC:
0
AN:
10260
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67572
Other (OTH)
AF:
AC:
0
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.650
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<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.:
ClinVar
Not reported inComputational 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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