8-127416910-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001159542.3(POU5F1B):c.1044C>T(p.Ser348=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000075 in 1,600,704 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000069 ( 0 hom. )
Consequence
POU5F1B
NM_001159542.3 synonymous
NM_001159542.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.409
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]
PCAT1 (HGNC:43022): (prostate cancer associated transcript 1) This gene produces a long non-coding RNA that promotes cell proliferation and is upregulated in prostate, colorectal, and other cancers. This RNA negatively regulates the BRCA2 tumor suppressor protein and positively regulates Myc oncoprotein. It contains binding sites for microRNAs, and may act as a sponge for microRNAs that regulate cell growth pathways. [provided by RefSeq, Dec 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 8-127416910-C-T is Benign according to our data. Variant chr8-127416910-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2658808.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.409 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POU5F1B | NM_001159542.3 | c.1044C>T | p.Ser348= | synonymous_variant | 1/1 | ENST00000696633.1 | |
CASC8 | NR_117100.1 | n.1176+3919G>A | intron_variant, non_coding_transcript_variant | ||||
POU5F1B | NM_001395745.1 | c.1044C>T | p.Ser348= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POU5F1B | ENST00000696633.1 | c.1044C>T | p.Ser348= | synonymous_variant | 1/1 | NM_001159542.3 | P1 | ||
CASC8 | ENST00000502082.5 | n.1176+3919G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.00000879 AC: 2AN: 227586Hom.: 0 AF XY: 0.00000819 AC XY: 1AN XY: 122148
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GnomAD4 exome AF: 0.00000690 AC: 10AN: 1448534Hom.: 0 Cov.: 109 AF XY: 0.00000696 AC XY: 5AN XY: 718884
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2022 | POU5F1B: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at