12-51245986-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_001031628.2(SMAGP):c.249G>A(p.Glu83Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001031628.2 synonymous
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMAGP | NM_001031628.2 | c.249G>A | p.Glu83Glu | synonymous_variant | Exon 4 of 4 | ENST00000603798.6 | NP_001026798.1 | |
SMAGP | NM_001033873.1 | c.249G>A | p.Glu83Glu | synonymous_variant | Exon 4 of 4 | NP_001029045.1 | ||
DAZAP2 | NM_001136269.2 | c.379-75C>T | intron_variant | Intron 3 of 3 | NP_001129741.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249216Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135200
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461664Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727116
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at