19-464035-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_182577.3(ODF3L2):c.679C>T(p.Arg227Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000119 in 1,597,184 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R227Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_182577.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ODF3L2 | NM_182577.3 | c.679C>T | p.Arg227Trp | missense_variant | 4/4 | ENST00000315489.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CIMAP1D | ENST00000315489.5 | c.679C>T | p.Arg227Trp | missense_variant | 4/4 | 1 | NM_182577.3 | P2 | |
CIMAP1D | ENST00000382696.7 | c.571C>T | p.Arg191Trp | missense_variant | 3/3 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000265 AC: 4AN: 150910Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000104 AC: 15AN: 1446274Hom.: 0 Cov.: 40 AF XY: 0.00000974 AC XY: 7AN XY: 718504
GnomAD4 genome ? AF: 0.0000265 AC: 4AN: 150910Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73676
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 12, 2023 | The c.679C>T (p.R227W) alteration is located in exon 4 (coding exon 4) of the ODF3L2 gene. This alteration results from a C to T substitution at nucleotide position 679, causing the arginine (R) at amino acid position 227 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at