chr3-87259754-T-TAA
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000306.4(POU1F1):c.*139_*140insTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000504 in 654,192 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000073 ( 1 hom., cov: 31)
Exomes 𝑓: 0.000044 ( 0 hom. )
Consequence
POU1F1
NM_000306.4 3_prime_UTR
NM_000306.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.45
Genes affected
POU1F1 (HGNC:9210): (POU class 1 homeobox 1) This gene encodes a member of the POU family of transcription factors that regulate mammalian development. The protein regulates expression of several genes involved in pituitary development and hormone expression. Mutations in this genes result in combined pituitary hormone deficiency. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POU1F1 | NM_000306.4 | c.*139_*140insTT | 3_prime_UTR_variant | 6/6 | ENST00000350375.7 | ||
POU1F1 | NM_001122757.3 | c.*139_*140insTT | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POU1F1 | ENST00000350375.7 | c.*139_*140insTT | 3_prime_UTR_variant | 6/6 | 1 | NM_000306.4 | P4 | ||
POU1F1 | ENST00000344265.8 | c.*139_*140insTT | 3_prime_UTR_variant | 6/6 | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000726 AC: 11AN: 151538Hom.: 1 Cov.: 31
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GnomAD4 exome AF: 0.0000438 AC: 22AN: 502538Hom.: 0 Cov.: 7 AF XY: 0.0000562 AC XY: 15AN XY: 267034
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GnomAD4 genome ? AF: 0.0000725 AC: 11AN: 151654Hom.: 1 Cov.: 31 AF XY: 0.0000675 AC XY: 5AN XY: 74100
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Combined Pituitary Hormone Deficiency, Recessive Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at