rs3094188

chr6-31174468-C-Achr6-31174468-C-Gchr6-31174468-C-T

Variant summary

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

The ENST00000441888.7(POU5F1):c.-184+6151G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 151,990 control chromosomes in the GnomAD database, including 35,543 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 0.68 (35543 hom., cov: 31)
• Consequence: POU5F1 ENST00000441888.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552

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]

PSORS1C3 (HGNC:17203): (psoriasis susceptibility 1 candidate 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSORS1C3	NR_152835.1	n.293-435G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POU5F1	ENST00000441888.7	c.-184+6151G>T		intron_variant		1
PSORS1C3	ENST00000412143.1	n.262-198G>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103495 AN: 151872 Hom.: 35504 Cov.: 31

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.682 AC: 103591 AN: 151990 Hom.: 35543 Cov.: 31 AF XY: 0.679 AC XY: 50450 AN XY: 74288

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.702

Gnomad4 ASJ AF: 0.802

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.714

Alfa AF: 0.658 Hom.: 59844

Bravo AF: 0.694

Asia WGS AF: 0.639 AC: 2224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.2
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3094188; hg19: chr6-31142245;