6-31171598-ACC-AC

Position:

• chr6-31171598-ACC-AC

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The ENST00000441888.7(POU5F1):​c.-183-5552del 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

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POU5F1	ENST00000441888.7	c.-183-5552del		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 69959 AN: 114816 Hom.: 16286 Cov.: 0 FAILED QC

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

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.584

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5875289; hg19: chr6-31139375;