9-92415316-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005014.3(OMD):āc.1102A>Gā(p.Thr368Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000675 in 1,613,754 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_005014.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OMD | NM_005014.3 | c.1102A>G | p.Thr368Ala | missense_variant | 3/3 | ENST00000375550.5 | NP_005005.1 | |
CENPP | NM_001012267.3 | c.564+35457T>C | intron_variant | ENST00000375587.8 | NP_001012267.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OMD | ENST00000375550.5 | c.1102A>G | p.Thr368Ala | missense_variant | 3/3 | 1 | NM_005014.3 | ENSP00000364700 | P1 | |
CENPP | ENST00000375587.8 | c.564+35457T>C | intron_variant | 1 | NM_001012267.3 | ENSP00000364737 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00104 AC: 158AN: 152162Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00104 AC: 260AN: 250964Hom.: 2 AF XY: 0.00106 AC XY: 144AN XY: 135656
GnomAD4 exome AF: 0.000639 AC: 934AN: 1461474Hom.: 3 Cov.: 31 AF XY: 0.000682 AC XY: 496AN XY: 727044
GnomAD4 genome AF: 0.00102 AC: 156AN: 152280Hom.: 3 Cov.: 32 AF XY: 0.000954 AC XY: 71AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 28, 2022 | The c.1102A>G (p.T368A) alteration is located in exon 3 (coding exon 2) of the OMD gene. This alteration results from a A to G substitution at nucleotide position 1102, causing the threonine (T) at amino acid position 368 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