chr6-31172311-T-C

Position:

• chr6-31172311-T-C

Variant summary

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

The ENST00000441888.7(POU5F1):​c.-183-6264A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 151,644 control chromosomes in the GnomAD database, including 29,614 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 0.62 (29614 hom., cov: 31)
• Consequence: POU5F1 ENST00000441888.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POU5F1	ENST00000441888.7	c.-183-6264A>G		intron_variant		1		ENSP00000389359

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94583 AN: 151526 Hom.: 29584 Cov.: 31

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.624 AC: 94655 AN: 151644 Hom.: 29614 Cov.: 31 AF XY: 0.627 AC XY: 46482 AN XY: 74096

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.632

Alfa AF: 0.604 Hom.: 3448

Bravo AF: 0.625

Asia WGS AF: 0.618 AC: 2151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3132519; hg19: chr6-31140088;