chr12-57793041-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005726.6(TSFM):c.539G>A(p.Gly180Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,614 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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. G180A) has been classified as Uncertain significance.
Frequency
Consequence
NM_005726.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSFM | NM_005726.6 | c.539G>A | p.Gly180Asp | missense_variant | 5/6 | ENST00000652027.2 | |
TSFM | NM_001172696.2 | c.602G>A | p.Gly201Asp | missense_variant | 6/7 | ||
TSFM | NM_001172697.2 | c.539G>A | p.Gly180Asp | missense_variant | 5/6 | ||
TSFM | NM_001172695.2 | c.484-3136G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSFM | ENST00000652027.2 | c.539G>A | p.Gly180Asp | missense_variant | 5/6 | NM_005726.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461394Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 726998
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74368
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at