chr17-31295887-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002544.5(OMG):c.445G>A(p.Glu149Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 1,614,060 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002544.5 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 | UniProt |
---|---|---|---|---|---|---|---|
OMG | NM_002544.5 | c.445G>A | p.Glu149Lys | missense_variant | 2/2 | ENST00000247271.5 | |
NF1 | NM_001042492.3 | c.4836-29933C>T | intron_variant | ENST00000358273.9 | |||
NF1 | NM_000267.3 | c.4773-29933C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OMG | ENST00000247271.5 | c.445G>A | p.Glu149Lys | missense_variant | 2/2 | 1 | NM_002544.5 | P1 | |
NF1 | ENST00000358273.9 | c.4836-29933C>T | intron_variant | 1 | NM_001042492.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250944Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135608
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461852Hom.: 0 Cov.: 32 AF XY: 0.0000303 AC XY: 22AN XY: 727226
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74414
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2022 | The c.445G>A (p.E149K) alteration is located in exon 2 (coding exon 1) of the OMG gene. This alteration results from a G to A substitution at nucleotide position 445, causing the glutamic acid (E) at amino acid position 149 to be replaced by a lysine (K). 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