rs754484224
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_003611.3(OFD1):āc.1469A>Gā(p.Glu490Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0000273 in 1,208,553 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 20 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E490K) has been classified as Uncertain significance.
Frequency
Consequence
NM_003611.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OFD1 | NM_003611.3 | c.1469A>G | p.Glu490Gly | missense_variant | 14/23 | ENST00000340096.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OFD1 | ENST00000340096.11 | c.1469A>G | p.Glu490Gly | missense_variant | 14/23 | 1 | NM_003611.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000902 AC: 1AN: 110865Hom.: 0 Cov.: 22 AF XY: 0.0000302 AC XY: 1AN XY: 33061
GnomAD3 exomes AF: 0.0000436 AC: 8AN: 183341Hom.: 0 AF XY: 0.0000590 AC XY: 4AN XY: 67779
GnomAD4 exome AF: 0.0000292 AC: 32AN: 1097636Hom.: 0 Cov.: 32 AF XY: 0.0000523 AC XY: 19AN XY: 363018
GnomAD4 genome ? AF: 0.00000902 AC: 1AN: 110917Hom.: 0 Cov.: 22 AF XY: 0.0000302 AC XY: 1AN XY: 33123
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 14, 2015 | - - |
Familial aplasia of the vermis;C1510460:Orofaciodigital syndrome I Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 23, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at