6-31173432-A-G

Variant summary

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

The ENST00000441888.7(POU5F1):​c.-184+7187T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.785 in 152,242 control chromosomes in the GnomAD database, including 47,166 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 0.79 ( 47166 hom., cov: 34)

Consequence

POU5F1
ENST00000441888.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.205
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
POU5F1ENST00000441888.7 linkuse as main transcriptc.-184+7187T>C intron_variant 1 ENSP00000389359

Frequencies

GnomAD3 genomes
AF:
0.785
AC:
119403
AN:
152124
Hom.:
47109
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.871
Gnomad AMI
AF:
0.800
Gnomad AMR
AF:
0.784
Gnomad ASJ
AF:
0.727
Gnomad EAS
AF:
0.720
Gnomad SAS
AF:
0.701
Gnomad FIN
AF:
0.764
Gnomad MID
AF:
0.845
Gnomad NFE
AF:
0.749
Gnomad OTH
AF:
0.811
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.785
AC:
119514
AN:
152242
Hom.:
47166
Cov.:
34
AF XY:
0.783
AC XY:
58281
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.871
Gnomad4 AMR
AF:
0.784
Gnomad4 ASJ
AF:
0.727
Gnomad4 EAS
AF:
0.721
Gnomad4 SAS
AF:
0.701
Gnomad4 FIN
AF:
0.764
Gnomad4 NFE
AF:
0.749
Gnomad4 OTH
AF:
0.809
Alfa
AF:
0.755
Hom.:
16707
Bravo
AF:
0.791
Asia WGS
AF:
0.747
AC:
2600
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
7.5
DANN
Benign
0.83

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: rs2269712; hg19: chr6-31141209; API