chr6-31171713-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000441888.7(POU5F1):c.-183-5666G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,434 control chromosomes in the GnomAD database, including 13,404 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.42 ( 13404 hom., cov: 28)
Consequence
POU5F1
ENST00000441888.7 intron
ENST00000441888.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.318
Publications
24 publications found
Genes affected
POU5F1 (HGNC:9221): (POU class 5 homeobox 1) This gene encodes a transcription factor containing a POU homeodomain that plays a key role in embryonic development and stem cell pluripotency. Aberrant expression of this gene in adult tissues is associated with tumorigenesis. This gene can participate in a translocation with the Ewing's sarcoma gene on chromosome 21, which also leads to tumor formation. Alternative splicing, as well as usage of alternative AUG and non-AUG translation initiation codons, results in multiple isoforms. One of the AUG start codons is polymorphic in human populations. Related pseudogenes have been identified on chromosomes 1, 3, 8, 10, and 12. [provided by RefSeq, Oct 2013]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|
Ensembl
Frequencies
GnomAD3 genomes AF: 0.420 AC: 63545AN: 151316Hom.: 13401 Cov.: 28 show subpopulations
GnomAD3 genomes
AF:
AC:
63545
AN:
151316
Hom.:
Cov.:
28
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.420 AC: 63569AN: 151434Hom.: 13404 Cov.: 28 AF XY: 0.414 AC XY: 30625AN XY: 73968 show subpopulations
GnomAD4 genome
AF:
AC:
63569
AN:
151434
Hom.:
Cov.:
28
AF XY:
AC XY:
30625
AN XY:
73968
show subpopulations
African (AFR)
AF:
AC:
18300
AN:
41218
American (AMR)
AF:
AC:
6579
AN:
15204
Ashkenazi Jewish (ASJ)
AF:
AC:
1221
AN:
3468
East Asian (EAS)
AF:
AC:
1955
AN:
5118
South Asian (SAS)
AF:
AC:
1713
AN:
4798
European-Finnish (FIN)
AF:
AC:
3760
AN:
10468
Middle Eastern (MID)
AF:
AC:
116
AN:
294
European-Non Finnish (NFE)
AF:
AC:
28704
AN:
67854
Other (OTH)
AF:
AC:
820
AN:
2102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.508
Heterozygous variant carriers
0
1842
3685
5527
7370
9212
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
606
1212
1818
2424
3030
<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:
Asia WGS
AF:
AC:
1307
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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