rs749657986
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_024589.3(ROGDI):c.531+5G>T variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000142 in 1,548,222 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024589.3 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ROGDI | NM_024589.3 | c.531+5G>T | splice_donor_5th_base_variant, intron_variant | ENST00000322048.12 | NP_078865.1 | |||
ROGDI | XM_006720947.5 | c.531+5G>T | splice_donor_5th_base_variant, intron_variant | XP_006721010.1 | ||||
ROGDI | XM_047434636.1 | c.261+5G>T | splice_donor_5th_base_variant, intron_variant | XP_047290592.1 | ||||
ROGDI | NR_046480.2 | n.538+5G>T | splice_donor_5th_base_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ROGDI | ENST00000322048.12 | c.531+5G>T | splice_donor_5th_base_variant, intron_variant | 1 | NM_024589.3 | ENSP00000322832 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000150 AC: 21AN: 1396022Hom.: 0 Cov.: 31 AF XY: 0.0000174 AC XY: 12AN XY: 689870
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74348
ClinVar
Submissions by phenotype
Amelocerebrohypohidrotic syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Apr 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at