rs762853362
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_024589.3(ROGDI):c.819C>T(p.Asp273=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,956 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 37)
Exomes 𝑓: 0.000010 ( 0 hom. )
Consequence
ROGDI
NM_024589.3 synonymous
NM_024589.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.158
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 Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
?
Variant 16-4797717-G-A is Benign according to our data. Variant chr16-4797717-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 697478.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.158 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ROGDI | NM_024589.3 | c.819C>T | p.Asp273= | synonymous_variant | 10/11 | ENST00000322048.12 | |
ROGDI | XM_006720947.5 | c.840C>T | p.Asp280= | synonymous_variant | 10/11 | ||
ROGDI | XM_047434636.1 | c.570C>T | p.Asp190= | synonymous_variant | 8/9 | ||
ROGDI | NR_046480.2 | n.826C>T | non_coding_transcript_exon_variant | 9/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ROGDI | ENST00000322048.12 | c.819C>T | p.Asp273= | synonymous_variant | 10/11 | 1 | NM_024589.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 37
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GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251220Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135842
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GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461740Hom.: 0 Cov.: 37 AF XY: 0.00000825 AC XY: 6AN XY: 727182
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GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 37 AF XY: 0.00 AC XY: 0AN XY: 74360
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Amelocerebrohypohidrotic syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
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Name
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Benign
CADD
Benign
DANN
Benign
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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