5-141515084-C-CAG
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_005219.5(DIAPH1):c.*1766_*1767insCT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00378 in 152,280 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.0038 ( 5 hom., cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
DIAPH1
NM_005219.5 3_prime_UTR
NM_005219.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.693
Genes affected
DIAPH1 (HGNC:2876): (diaphanous related formin 1) This gene is a homolog of the Drosophila diaphanous gene, and has been linked to autosomal dominant, fully penetrant, nonsyndromic sensorineural progressive low-frequency hearing loss. Actin polymerization involves proteins known to interact with diaphanous protein in Drosophila and mouse. It has therefore been speculated that this gene may have a role in the regulation of actin polymerization in hair cells of the inner ear. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP6
?
Variant 5-141515084-C-CAG is Benign according to our data. Variant chr5-141515084-C-CAG is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 351253.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Benign=1}.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00378 (576/152280) while in subpopulation AMR AF= 0.011 (168/15298). AF 95% confidence interval is 0.00963. There are 5 homozygotes in gnomad4. There are 278 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 576 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DIAPH1 | NM_005219.5 | c.*1766_*1767insCT | 3_prime_UTR_variant | 28/28 | ENST00000389054.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DIAPH1 | ENST00000389054.8 | c.*1766_*1767insCT | 3_prime_UTR_variant | 28/28 | 5 | NM_005219.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00379 AC: 576AN: 152162Hom.: 5 Cov.: 33
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 442Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 264
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GnomAD4 genome ? AF: 0.00378 AC: 576AN: 152280Hom.: 5 Cov.: 33 AF XY: 0.00373 AC XY: 278AN XY: 74466
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Nonsyndromic Hearing Loss, Mixed Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | DIAPH1: BS1, BS2 - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at