rs16902124

Variant summary

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

The ENST00000645438.1(POU5F1B):​c.-560+5537G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0734 in 152,228 control chromosomes in the GnomAD database, including 602 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 0.073 ( 602 hom., cov: 32)

Consequence

POU5F1B
ENST00000645438.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.21
Variant links:
Genes affected
POU5F1B (HGNC:9223): (POU class 5 homeobox 1B) This intronless gene was thought to be a transcribed pseudogene of POU class 5 homeobox 1, however, it has been reported that this gene can encode a functional protein. The encoded protein is nearly the same length as and highly similar to the POU class 5 homeobox 1 transcription factor, has been shown to be a weak transcriptional activator and may play a role in carcinogenesis and eye development. [provided by RefSeq, Apr 2009]

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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=-0.86).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CASC21NR_117099.1 linkuse as main transcriptn.457+5537G>A intron_variant
CASC8NR_117100.1 linkuse as main transcriptn.1177-54912C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CASC8ENST00000501396.5 linkuse as main transcriptn.547-21818C>T intron_variant 1
CASC8ENST00000502082.5 linkuse as main transcriptn.1177-54912C>T intron_variant 1
PCAT1ENST00000521586.2 linkuse as main transcriptn.289+5537G>A intron_variant 1

Frequencies

GnomAD3 genomes
AF:
0.0733
AC:
11157
AN:
152110
Hom.:
601
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0911
Gnomad AMI
AF:
0.0230
Gnomad AMR
AF:
0.174
Gnomad ASJ
AF:
0.0479
Gnomad EAS
AF:
0.131
Gnomad SAS
AF:
0.0834
Gnomad FIN
AF:
0.0157
Gnomad MID
AF:
0.0506
Gnomad NFE
AF:
0.0456
Gnomad OTH
AF:
0.0851
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0734
AC:
11173
AN:
152228
Hom.:
602
Cov.:
32
AF XY:
0.0722
AC XY:
5376
AN XY:
74426
show subpopulations
Gnomad4 AFR
AF:
0.0910
Gnomad4 AMR
AF:
0.174
Gnomad4 ASJ
AF:
0.0479
Gnomad4 EAS
AF:
0.131
Gnomad4 SAS
AF:
0.0839
Gnomad4 FIN
AF:
0.0157
Gnomad4 NFE
AF:
0.0457
Gnomad4 OTH
AF:
0.0842
Alfa
AF:
0.0620
Hom.:
349
Bravo
AF:
0.0883
Asia WGS
AF:
0.109
AC:
377
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
5.0
DANN
Benign
0.81

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: rs16902124; hg19: chr8-128357218; API