19-464140-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_182577.3(CIMAP1D):c.574G>A(p.Ala192Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000946 in 799,032 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_182577.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CIMAP1D | NM_182577.3 | c.574G>A | p.Ala192Thr | missense_variant | 4/4 | ENST00000315489.5 | NP_872383.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ODF3L2 | ENST00000315489.5 | c.574G>A | p.Ala192Thr | missense_variant | 4/4 | 1 | NM_182577.3 | ENSP00000318029.2 | ||
ODF3L2 | ENST00000382696.7 | c.466G>A | p.Ala156Thr | missense_variant | 3/3 | 1 | ENSP00000372143.2 | |||
ODF3L2 | ENST00000591681.3 | n.*27G>A | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00391 AC: 91AN: 23298Hom.: 0 Cov.: 0
GnomAD4 exome AF: 0.000859 AC: 666AN: 775716Hom.: 9 Cov.: 24 AF XY: 0.000833 AC XY: 309AN XY: 370860
GnomAD4 genome AF: 0.00386 AC: 90AN: 23316Hom.: 0 Cov.: 0 AF XY: 0.00413 AC XY: 47AN XY: 11378
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at