Variant rs13409 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4BA1

The ENST00000259915.13(POU5F1):c.*238C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 1,151,312 control chromosomes in the GnomAD database, including 110,166 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 0.44 ( 14696 hom., cov: 32)

Exomes 𝑓: 0.43 ( 95470 hom. )

Consequence

POU5F1
ENST00000259915.13 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.82

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]

POU5F1 links:

TCF19 (HGNC:11629): (transcription factor 19) This gene encodes a protein that contains a PHD-type zinc finger domain and likely functions as a transcription factor. The encoded protein plays a role proliferation and apoptosis of pancreatic beta cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

TCF19 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.14).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
POU5F1	NM_002701.6 linkuse as main transcript	c.*238C>T	3_prime_UTR_variant	5/5	ENST00000259915.13	NP_002692.2
POU5F1	NM_001173531.3 linkuse as main transcript	c.*238C>T	3_prime_UTR_variant	5/5		NP_001167002.1
POU5F1	NM_001285986.2 linkuse as main transcript	c.*238C>T	3_prime_UTR_variant	3/3		NP_001272915.1
POU5F1	NM_203289.6 linkuse as main transcript	c.*238C>T	3_prime_UTR_variant	4/4		NP_976034.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POU5F1	ENST00000259915.13 linkuse as main transcript	c.*238C>T		3_prime_UTR_variant	5/5	1	NM_002701.6	ENSP00000259915	P1	Q01860-1

Frequencies

GnomAD3 genomes

AF:

0.439

AC:

66531

AN:

151722

Hom.:

14690

Cov.:

show subpopulations

Gnomad AFR

AF:

0.479

Gnomad AMI

AF:

0.448

Gnomad AMR

AF:

0.453

Gnomad ASJ

AF:

0.393

Gnomad EAS

AF:

0.380

Gnomad SAS

AF:

0.375

Gnomad FIN

AF:

0.361

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.434

Gnomad OTH

AF:

0.414

GnomAD4 exome

AF:

0.434

AC:

433392

AN:

999472

Hom.:

95470

Cov.:

AF XY:

0.431

AC XY:

213177

AN XY:

494714

show subpopulations

Gnomad4 AFR exome

AF:

0.479

Gnomad4 AMR exome

AF:

0.446

Gnomad4 ASJ exome

AF:

0.406

Gnomad4 EAS exome

AF:

0.360

Gnomad4 SAS exome

AF:

0.384

Gnomad4 FIN exome

AF:

0.365

Gnomad4 NFE exome

AF:

0.444

Gnomad4 OTH exome

AF:

0.429

GnomAD4 genome

AF:

0.438

AC:

66564

AN:

151840

Hom.:

14696

Cov.:

AF XY:

0.433

AC XY:

32130

AN XY:

74212

show subpopulations

Gnomad4 AFR

AF:

0.479

Gnomad4 AMR

AF:

0.453

Gnomad4 ASJ

AF:

0.393

Gnomad4 EAS

AF:

0.381

Gnomad4 SAS

AF:

0.373

Gnomad4 FIN

AF:

0.361

Gnomad4 NFE

AF:

0.434

Gnomad4 OTH

AF:

0.413

Alfa

AF:

0.429

Hom.:

4716

Bravo

AF:

0.448

Asia WGS

AF:

0.398

AC:

1381

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.14

CADD

Benign

DANN

Benign

0.93

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over