rs114103417
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_024589.3(ROGDI):c.433-15C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00161 in 1,546,160 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0075 ( 5 hom., cov: 33)
Exomes 𝑓: 0.00097 ( 19 hom. )
Consequence
ROGDI
NM_024589.3 splice_polypyrimidine_tract, intron
NM_024589.3 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.339
Genes affected
ROGDI (HGNC:29478): (rogdi atypical leucine zipper) Involved in brain development; neurogenesis; and odontogenesis of dentin-containing tooth. Located in nuclear envelope. Implicated in Kohlschutter-Tonz syndrome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 16-4798682-G-A is Benign according to our data. Variant chr16-4798682-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 261743.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-4798682-G-A is described in Lovd as [Likely_benign].
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00745 (1135/152250) while in subpopulation AFR AF= 0.023 (957/41544). AF 95% confidence interval is 0.0218. There are 5 homozygotes in gnomad4. There are 560 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ROGDI | NM_024589.3 | c.433-15C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000322048.12 | |||
ROGDI | XM_006720947.5 | c.433-15C>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
ROGDI | XM_047434636.1 | c.163-15C>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
ROGDI | NR_046480.2 | n.440-15C>T | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ROGDI | ENST00000322048.12 | c.433-15C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_024589.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00738 AC: 1123AN: 152132Hom.: 4 Cov.: 33
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GnomAD3 exomes AF: 0.00226 AC: 350AN: 155038Hom.: 1 AF XY: 0.00182 AC XY: 150AN XY: 82528
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GnomAD4 exome AF: 0.000974 AC: 1357AN: 1393910Hom.: 19 Cov.: 31 AF XY: 0.000921 AC XY: 634AN XY: 688722
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Amelocerebrohypohidrotic syndrome Benign:3
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. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Dec 01, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Name
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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