Variant rs1062630 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002701.6(POU5F1):c.291C>T(p.Gly97=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 1,612,544 control chromosomes in the GnomAD database, including 44,585 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 0.22 ( 3905 hom., cov: 34)

Exomes 𝑓: 0.23 ( 40680 hom. )

Consequence

POU5F1
NM_002701.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.220

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BP7

Synonymous conserved (PhyloP=-0.22 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POU5F1	NM_002701.6 linkuse as main transcript	c.291C>T	p.Gly97=	synonymous_variant	1/5	ENST00000259915.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POU5F1	ENST00000259915.13 linkuse as main transcript	c.291C>T	p.Gly97=	synonymous_variant	1/5	1	NM_002701.6	P1	Q01860-1
POU5F1	ENST00000441888.7 linkuse as main transcript	c.-183-4283C>T		intron_variant		1
POU5F1	ENST00000461401.1 linkuse as main transcript	n.329C>T		non_coding_transcript_exon_variant	1/2	1

Frequencies

GnomAD3 genomes

AF:

0.220

AC:

33515

AN:

152052

Hom.:

3900

Cov.:

show subpopulations

Gnomad AFR

AF:

0.267

Gnomad AMI

AF:

0.341

Gnomad AMR

AF:

0.160

Gnomad ASJ

AF:

0.268

Gnomad EAS

AF:

0.0408

Gnomad SAS

AF:

0.129

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.235

Gnomad OTH

AF:

0.215

GnomAD3 exomes

AF:

0.182

AC:

44705

AN:

245770

Hom.:

4772

AF XY:

0.182

AC XY:

24460

AN XY:

134092

show subpopulations

Gnomad AFR exome

AF:

0.268

Gnomad AMR exome

AF:

0.123

Gnomad ASJ exome

AF:

0.282

Gnomad EAS exome

AF:

0.0319

Gnomad SAS exome

AF:

0.141

Gnomad FIN exome

AF:

0.135

Gnomad NFE exome

AF:

0.224

Gnomad OTH exome

AF:

0.201

GnomAD4 exome

AF:

0.228

AC:

333211

AN:

1460374

Hom.:

40680

Cov.:

AF XY:

0.225

AC XY:

163654

AN XY:

726490

show subpopulations

Gnomad4 AFR exome

AF:

0.271

Gnomad4 AMR exome

AF:

0.127

Gnomad4 ASJ exome

AF:

0.283

Gnomad4 EAS exome

AF:

0.0222

Gnomad4 SAS exome

AF:

0.140

Gnomad4 FIN exome

AF:

0.139

Gnomad4 NFE exome

AF:

0.248

Gnomad4 OTH exome

AF:

0.233

GnomAD4 genome

AF:

0.220

AC:

33529

AN:

152170

Hom.:

3905

Cov.:

AF XY:

0.211

AC XY:

15729

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.267

Gnomad4 AMR

AF:

0.159

Gnomad4 ASJ

AF:

0.268

Gnomad4 EAS

AF:

0.0409

Gnomad4 SAS

AF:

0.129

Gnomad4 FIN

AF:

0.137

Gnomad4 NFE

AF:

0.235

Gnomad4 OTH

AF:

0.212

Alfa

AF:

0.232

Hom.:

1972

Bravo

AF:

0.224

Asia WGS

AF:

0.0840

AC:

294

AN:

3478

EpiCase

AF:

0.238

EpiControl

AF:

0.225

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

6.1

DANN

Benign

0.86

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