chr19-464143-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_182577.3(ODF3L2):c.571C>G(p.Pro191Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign 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. P191R) has been classified as Uncertain significance.
Frequency
Consequence
NM_182577.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ODF3L2 | NM_182577.3 | c.571C>G | p.Pro191Ala | missense_variant | 4/4 | ENST00000315489.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CIMAP1D | ENST00000315489.5 | c.571C>G | p.Pro191Ala | missense_variant | 4/4 | 1 | NM_182577.3 | P2 | |
CIMAP1D | ENST00000382696.7 | c.463C>G | p.Pro155Ala | missense_variant | 3/3 | 1 | A2 | ||
CIMAP1D | ENST00000591681.3 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 6AN: 145398Hom.: 0 Cov.: 31 FAILED QC
GnomAD3 exomes AF: 0.0000845 AC: 7AN: 82838Hom.: 0 AF XY: 0.0000911 AC XY: 4AN XY: 43928
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000118 AC: 48AN: 407984Hom.: 0 Cov.: 0 AF XY: 0.000115 AC XY: 25AN XY: 216946
GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000412 AC: 6AN: 145536Hom.: 0 Cov.: 31 AF XY: 0.0000565 AC XY: 4AN XY: 70816
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 26, 2023 | The c.571C>G (p.P191A) alteration is located in exon 4 (coding exon 4) of the ODF3L2 gene. This alteration results from a C to G substitution at nucleotide position 571, causing the proline (P) at amino acid position 191 to be replaced by an alanine (A). 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