rs375517608
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_024589.3(ROGDI):c.417C>T(p.Gly139=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000679 in 1,613,086 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.00034 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00071 ( 17 hom. )
Consequence
ROGDI
NM_024589.3 synonymous
NM_024589.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.847
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 -19 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
?
Variant 16-4799701-G-A is Benign according to our data. Variant chr16-4799701-G-A is described in ClinVar as [Benign]. Clinvar id is 461611.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-4799701-G-A is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=-0.847 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000342 (52/152266) while in subpopulation SAS AF= 0.0101 (49/4830). AF 95% confidence interval is 0.00788. There are 1 homozygotes in gnomad4. There are 44 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome4 at 17 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ROGDI | NM_024589.3 | c.417C>T | p.Gly139= | synonymous_variant | 6/11 | ENST00000322048.12 | |
ROGDI | XM_006720947.5 | c.417C>T | p.Gly139= | synonymous_variant | 6/11 | ||
ROGDI | XM_047434636.1 | c.147C>T | p.Gly49= | synonymous_variant | 4/9 | ||
ROGDI | NR_046480.2 | n.424C>T | non_coding_transcript_exon_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ROGDI | ENST00000322048.12 | c.417C>T | p.Gly139= | synonymous_variant | 6/11 | 1 | NM_024589.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000322 AC: 49AN: 152148Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00138 AC: 345AN: 249762Hom.: 5 AF XY: 0.00175 AC XY: 237AN XY: 135092
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GnomAD4 exome AF: 0.000714 AC: 1043AN: 1460820Hom.: 17 Cov.: 29 AF XY: 0.000992 AC XY: 721AN XY: 726688
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GnomAD4 genome ? AF: 0.000342 AC: 52AN: 152266Hom.: 1 Cov.: 33 AF XY: 0.000591 AC XY: 44AN XY: 74452
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
ROGDI-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 02, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | ROGDI: BP4, BP7, BS1, BS2 - |
Amelocerebrohypohidrotic syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 17, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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