rs753364652
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_031448.6(C19orf12):c.238C>T(p.Leu80=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000157 in 1,461,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L80L) has been classified as Likely benign.
Frequency
Consequence
NM_031448.6 synonymous
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 |
---|---|---|---|---|---|---|---|
C19orf12 | NM_031448.6 | c.238C>T | p.Leu80= | synonymous_variant | 3/3 | ENST00000323670.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C19orf12 | ENST00000323670.14 | c.238C>T | p.Leu80= | synonymous_variant | 3/3 | 2 | NM_031448.6 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249912Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135200
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461888Hom.: 0 Cov.: 37 AF XY: 0.0000179 AC XY: 13AN XY: 727248
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 43 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at