rs1554264613
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Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 10P and 1B. PM2PP5_Very_StrongBP4
The variant allele was found at a frequency of 0.00000657 in 152,188 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 Pathogenic (★★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.407
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 6-99593111-G-C is Pathogenic according to our data. Variant chr6-99593111-G-C is described in ClinVar as [Pathogenic]. Clinvar id is 446240.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-99593111-G-C is described in Lovd as [Pathogenic]. Variant chr6-99593111-G-C is described in Lovd as [Likely_pathogenic].
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8). . Strength limited to SUPPORTING due to the PP5.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| use as main transcript | n.99593111G>C | intergenic_region |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74348
GnomAD4 genome
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Bravo
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Pathogenic:3
| Pathogenic, criteria provided, single submitter | clinical testing | Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen | Oct 23, 2020 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 18, 2023 | This variant occurs in a non-coding region of the PRDM13 gene. It does not change the encoded amino acid sequence of the PRDM13 protein. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with North Carolina macular dystrophy (PMID: 26507665, 27551809, 31043363, 31814698). It has also been observed to segregate with disease in related individuals. This variant is also known as V2 or chromosome 6: 99,593,111 (G>C) NC_000006.11(GRCh38):g.100040987G>C. For these reasons, this variant has been classified as Pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | PRDM13: PP1:Strong, PM1, PM2, PS4:Moderate - |
North Carolina macular dystrophy Pathogenic:1
| Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 29, 2019 | - - |
Retinal dystrophy Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg | Jan 01, 2023 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at