9-92415238-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005014.3(OMD):c.1180G>A(p.Asp394Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000359 in 1,613,642 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
Frequency
Consequence
NM_005014.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OMD | ENST00000375550.5 | c.1180G>A | p.Asp394Asn | missense_variant | Exon 3 of 3 | 1 | NM_005014.3 | ENSP00000364700.4 | ||
CENPP | ENST00000375587.8 | c.564+35379C>T | intron_variant | Intron 5 of 7 | 1 | NM_001012267.3 | ENSP00000364737.3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251002Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135658
GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461504Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727064
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1180G>A (p.D394N) alteration is located in exon 3 (coding exon 2) of the OMD gene. This alteration results from a G to A substitution at nucleotide position 1180, causing the aspartic acid (D) at amino acid position 394 to be replaced by an asparagine (N). 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