rs17190839

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000441888.7(POU5F1):​c.-183-4883C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0724 in 152,132 control chromosomes in the GnomAD database, including 658 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 0.072 ( 658 hom., cov: 32)

Consequence

POU5F1
ENST00000441888.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.775
Variant links:
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.31170930G>A intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
POU5F1ENST00000441888.7 linkuse as main transcriptc.-183-4883C>T intron_variant 1 ENSP00000389359.2 F2Z381

Frequencies

GnomAD3 genomes
AF:
0.0724
AC:
11009
AN:
152014
Hom.:
657
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.158
Gnomad AMI
AF:
0.0241
Gnomad AMR
AF:
0.0414
Gnomad ASJ
AF:
0.0444
Gnomad EAS
AF:
0.155
Gnomad SAS
AF:
0.0383
Gnomad FIN
AF:
0.0528
Gnomad MID
AF:
0.0443
Gnomad NFE
AF:
0.0287
Gnomad OTH
AF:
0.0722
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0724
AC:
11017
AN:
152132
Hom.:
658
Cov.:
32
AF XY:
0.0731
AC XY:
5439
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.158
Gnomad4 AMR
AF:
0.0413
Gnomad4 ASJ
AF:
0.0444
Gnomad4 EAS
AF:
0.154
Gnomad4 SAS
AF:
0.0384
Gnomad4 FIN
AF:
0.0528
Gnomad4 NFE
AF:
0.0287
Gnomad4 OTH
AF:
0.0720
Alfa
AF:
0.0513
Hom.:
44
Bravo
AF:
0.0780
Asia WGS
AF:
0.0930
AC:
323
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
3.6
DANN
Benign
0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17190839; hg19: chr6-31138707; API