rs113858060
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_024589.3(ROGDI):c.117+10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00122 in 1,566,322 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0067 ( 9 hom., cov: 33)
Exomes 𝑓: 0.00063 ( 17 hom. )
Consequence
ROGDI
NM_024589.3 intron
NM_024589.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.306
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=-0.76).
BP6
?
Variant 16-4802372-G-A is Benign according to our data. Variant chr16-4802372-G-A is described in ClinVar as [Benign]. Clinvar id is 416248.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-4802372-G-A is described in Lovd as [Likely_benign].
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00674 (1026/152242) while in subpopulation AFR AF= 0.0235 (976/41572). AF 95% confidence interval is 0.0223. There are 9 homozygotes in gnomad4. There are 443 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ROGDI | NM_024589.3 | c.117+10C>T | intron_variant | ENST00000322048.12 | |||
ROGDI | XM_006720947.5 | c.117+10C>T | intron_variant | ||||
ROGDI | XM_047434636.1 | c.-99+10C>T | intron_variant | ||||
ROGDI | NR_046480.2 | n.179+10C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ROGDI | ENST00000322048.12 | c.117+10C>T | intron_variant | 1 | NM_024589.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00674 AC: 1025AN: 152124Hom.: 9 Cov.: 33
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GnomAD3 exomes AF: 0.00168 AC: 299AN: 178084Hom.: 2 AF XY: 0.00122 AC XY: 120AN XY: 98040
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GnomAD4 exome AF: 0.000627 AC: 886AN: 1414080Hom.: 17 Cov.: 31 AF XY: 0.000555 AC XY: 389AN XY: 701446
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GnomAD4 genome ? AF: 0.00674 AC: 1026AN: 152242Hom.: 9 Cov.: 33 AF XY: 0.00595 AC XY: 443AN XY: 74446
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 20, 2017 | - - |
Amelocerebrohypohidrotic syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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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