rs186990152
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_000307.5(POU3F4):c.798G>A(p.Pro266Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,209,968 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000071 ( 0 hom., 5 hem., cov: 23)
Exomes 𝑓: 0.000031 ( 0 hom. 11 hem. )
Consequence
POU3F4
NM_000307.5 synonymous
NM_000307.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.298
Genes affected
POU3F4 (HGNC:9217): (POU class 3 homeobox 4) This gene encodes a member of the POU-III class of neural transcription factors. This family member plays a role in inner ear development. The protein is thought to be involved in the mediation of epigenetic signals which induce striatal neuron-precursor differentiation. Mutations in this gene are associated with X chromosome-linked nonsyndromic mixed deafness. [provided by RefSeq, Dec 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
Variant X-83509122-G-A is Benign according to our data. Variant chrX-83509122-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 227855.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.298 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 5 Mitochondrial gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POU3F4 | NM_000307.5 | c.798G>A | p.Pro266Pro | synonymous_variant | 1/1 | ENST00000644024.2 | NP_000298.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
POU3F4 | ENST00000644024.2 | c.798G>A | p.Pro266Pro | synonymous_variant | 1/1 | NM_000307.5 | ENSP00000495996.1 | |||
ENSG00000279437 | ENST00000625081.1 | n.93C>T | non_coding_transcript_exon_variant | 1/1 | 6 |
Frequencies
GnomAD3 genomes AF: 0.0000804 AC: 9AN: 111959Hom.: 0 Cov.: 23 AF XY: 0.000176 AC XY: 6AN XY: 34141
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GnomAD3 exomes AF: 0.0000110 AC: 2AN: 182586Hom.: 0 AF XY: 0.0000149 AC XY: 1AN XY: 67104
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GnomAD4 exome AF: 0.0000310 AC: 34AN: 1097961Hom.: 0 Cov.: 32 AF XY: 0.0000303 AC XY: 11AN XY: 363323
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GnomAD4 genome AF: 0.0000714 AC: 8AN: 112007Hom.: 0 Cov.: 23 AF XY: 0.000146 AC XY: 5AN XY: 34199
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 16, 2015 | p.Pro266Pro in exon 1 of POU3F4: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue and is not located w ithin the splice consensus sequence. This variant has been identified in 2/8295 African chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broad institute.org; dbSNP rs186990152). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at