X-154379690-G-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM5PP3BS2
The NM_000117.3(EMD):āc.83G>Cā(p.Gly28Ala) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000547 in 1,096,038 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G28R) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000117.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EMD | NM_000117.3 | c.83G>C | p.Gly28Ala | missense_variant, splice_region_variant | 2/6 | ENST00000369842.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EMD | ENST00000369842.9 | c.83G>C | p.Gly28Ala | missense_variant, splice_region_variant | 2/6 | 1 | NM_000117.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 25
GnomAD3 exomes AF: 0.00000578 AC: 1AN: 173152Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 64462
GnomAD4 exome AF: 0.00000547 AC: 6AN: 1096038Hom.: 0 Cov.: 31 AF XY: 0.00000828 AC XY: 3AN XY: 362336
GnomAD4 genome Cov.: 25
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at