6-31178062-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000441888.7(POU5F1):​c.-184+2557A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 152,000 control chromosomes in the GnomAD database, including 11,606 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 0.39 ( 11606 hom., cov: 32)

Consequence

POU5F1
ENST00000441888.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.515
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PSORS1C3NR_152835.1 linkuse as main transcriptn.293-4029A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
POU5F1ENST00000441888.7 linkuse as main transcriptc.-184+2557A>G intron_variant 1

Frequencies

GnomAD3 genomes
AF:
0.388
AC:
58999
AN:
151882
Hom.:
11605
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.346
Gnomad AMI
AF:
0.182
Gnomad AMR
AF:
0.450
Gnomad ASJ
AF:
0.425
Gnomad EAS
AF:
0.484
Gnomad SAS
AF:
0.407
Gnomad FIN
AF:
0.461
Gnomad MID
AF:
0.401
Gnomad NFE
AF:
0.382
Gnomad OTH
AF:
0.377
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.388
AC:
59027
AN:
152000
Hom.:
11606
Cov.:
32
AF XY:
0.395
AC XY:
29359
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.345
Gnomad4 AMR
AF:
0.450
Gnomad4 ASJ
AF:
0.425
Gnomad4 EAS
AF:
0.485
Gnomad4 SAS
AF:
0.407
Gnomad4 FIN
AF:
0.461
Gnomad4 NFE
AF:
0.382
Gnomad4 OTH
AF:
0.380
Alfa
AF:
0.386
Hom.:
11692
Bravo
AF:
0.385
Asia WGS
AF:
0.449
AC:
1558
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
1.1
DANN
Benign
0.61

Splicing

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.

Other links and lift over

dbSNP: rs3868542; hg19: chr6-31145839; API