rs61737151
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_002700.3(POU4F3):c.663C>A(p.Gly221=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000866 in 1,614,210 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0047 ( 5 hom., cov: 33)
Exomes 𝑓: 0.00047 ( 7 hom. )
Consequence
POU4F3
NM_002700.3 synonymous
NM_002700.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.611
Genes affected
POU4F3 (HGNC:9220): (POU class 4 homeobox 3) This gene encodes a member of the POU-domain family of transcription factors. POU-domain proteins have been observed to play important roles in control of cell identity in several systems. This protein is found in the retina and may play a role in determining or maintaining the identities of a small subset of visual system neurons. Defects in this gene are the cause of non-syndromic sensorineural deafness autosomal dominant type 15. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
?
Variant 5-146340090-C-A is Benign according to our data. Variant chr5-146340090-C-A is described in ClinVar as [Benign]. Clinvar id is 164983.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.611 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0047 (716/152330) while in subpopulation AFR AF= 0.0165 (687/41570). AF 95% confidence interval is 0.0155. There are 5 homozygotes in gnomad4. There are 339 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High AC in GnomAd at 710 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POU4F3 | NM_002700.3 | c.663C>A | p.Gly221= | synonymous_variant | 2/2 | ENST00000646991.2 | |
LOC127814297 | NM_001414499.1 | c.*532C>A | 3_prime_UTR_variant | 20/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POU4F3 | ENST00000646991.2 | c.663C>A | p.Gly221= | synonymous_variant | 2/2 | NM_002700.3 | P1 | ||
ENST00000515598.1 | n.404-32814G>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00466 AC: 710AN: 152212Hom.: 5 Cov.: 33
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GnomAD3 exomes AF: 0.00123 AC: 310AN: 251142Hom.: 1 AF XY: 0.000861 AC XY: 117AN XY: 135864
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GnomAD4 exome AF: 0.000467 AC: 682AN: 1461880Hom.: 7 Cov.: 31 AF XY: 0.000389 AC XY: 283AN XY: 727244
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 15, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 07, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 21, 2019 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 07, 2012 | Gly221Gly in Exon 02 of POU4F3: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue, is not located with in the splice consensus sequence, and has been identified in 1.5% (55/3738) of A frican American chromosomes from a broad population by the NHLBI Exome Sequencin g Project (http://evs.gs.washington.edu/EVS; dbSNP rs61737151). - |
Autosomal dominant nonsyndromic hearing loss 15 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
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