chr3-87259978-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000306.4(POU1F1):c.792C>T(p.Asn264=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,984 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: 32)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
POU1F1
NM_000306.4 synonymous
NM_000306.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.53
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 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=-0.53).
BP6
?
Variant 3-87259978-G-A is Benign according to our data. Variant chr3-87259978-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2992811.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.53 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POU1F1 | NM_000306.4 | c.792C>T | p.Asn264= | synonymous_variant | 6/6 | ENST00000350375.7 | |
POU1F1 | NM_001122757.3 | c.870C>T | p.Asn290= | synonymous_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POU1F1 | ENST00000350375.7 | c.792C>T | p.Asn264= | synonymous_variant | 6/6 | 1 | NM_000306.4 | P4 | |
POU1F1 | ENST00000344265.8 | c.870C>T | p.Asn290= | synonymous_variant | 6/6 | 5 | A1 | ||
POU1F1 | ENST00000561167.5 | c.567C>T | p.Asn189= | synonymous_variant | 5/5 | 5 | |||
POU1F1 | ENST00000560656.1 | c.*56C>T | 3_prime_UTR_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152132Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251060Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135666
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GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461852Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727220
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GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74298
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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 | Invitae | Jan 29, 2024 | - - |
Computational scores
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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