6-31171598-ACC-AC

Variant names:

• chr6-31171598-AC-A
• rs5875289
• ENST00000441888.7:c.-183-5552delG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000441888.7(POU5F1):​c.-183-5552delG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.61 (16304 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: POU5F1 ENST00000441888.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.678
• Publications: 2 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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POU5F1	ENST00000441888.7	c.-183-5552delG		intron_variant	Intron 1 of 4	1		ENSP00000389359.2

Frequencies

GnomAD3 genomes AF: 0.609 AC: 69959 AN: 114816 Hom.: 16286 Cov.: 0

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.586

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.609 AC: 70030 AN: 114928 Hom.: 16304 Cov.: 0 AF XY: 0.610 AC XY: 33396 AN XY: 54762

African (AFR) AF: 0.642 AC: 19224 AN: 29924

American (AMR) AF: 0.609 AC: 6689 AN: 10988

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 1838 AN: 2808

East Asian (EAS) AF: 0.557 AC: 2038 AN: 3658

South Asian (SAS) AF: 0.628 AC: 2087 AN: 3322

European-Finnish (FIN) AF: 0.592 AC: 4064 AN: 6868

Middle Eastern (MID) AF: 0.731 AC: 155 AN: 212

European-Non Finnish (NFE) AF: 0.594 AC: 32544 AN: 54806

Other (OTH) AF: 0.584 AC: 938 AN: 1606

Alfa AF: 0.538 Hom.: 836

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.68
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs5875289; hg19: chr6-31139375; COSMIC: COSV104389954; COSMIC: COSV104389954;