rs77493891
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_012213.3(MLYCD):c.776G>A(p.Gly259Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,614,144 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. 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. G259A) has been classified as Likely benign.
Frequency
Consequence
NM_012213.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MLYCD | NM_012213.3 | c.776G>A | p.Gly259Asp | missense_variant | 3/5 | ENST00000262430.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MLYCD | ENST00000262430.6 | c.776G>A | p.Gly259Asp | missense_variant | 3/5 | 1 | NM_012213.3 | P1 | |
MLYCD | ENST00000561562.5 | c.131G>A | p.Gly44Asp | missense_variant | 1/4 | 2 | |||
MLYCD | ENST00000566309.2 | c.86G>A | p.Gly29Asp | missense_variant, NMD_transcript_variant | 1/6 | 2 | |||
MLYCD | ENST00000563312.5 | c.86G>A | p.Gly29Asp | missense_variant, NMD_transcript_variant | 1/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249554Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135396
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461858Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727228
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152286Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74452
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at