chr6-31171675-T-C

Variant names:

• chr6-31171675-T-C
• rs879882
• ENST00000441888.7:c.-183-5628A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000441888.7(POU5F1):​c.-183-5628A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 148,632 control chromosomes in the GnomAD database, including 27,658 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 0.61 (27658 hom., cov: 24)
• Consequence: POU5F1 ENST00000441888.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

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.-183-5628A>G		intron_variant	Intron 1 of 4	1		ENSP00000389359.2

Frequencies

GnomAD3 genomes AF: 0.611 AC: 90698 AN: 148518 Hom.: 27650 Cov.: 24

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.700

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.611 AC: 90745 AN: 148632 Hom.: 27658 Cov.: 24 AF XY: 0.609 AC XY: 44042 AN XY: 72344

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.618

Alfa AF: 0.633 Hom.: 28654

Bravo AF: 0.604

Asia WGS AF: 0.547 AC: 1902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs879882; hg19: chr6-31139452;