X-135905333-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001381902.1(SAGE1):c.395C>T(p.Pro132Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000498 in 1,205,843 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P132S) has been classified as Likely benign.
Frequency
Consequence
NM_001381902.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SAGE1 | NM_001381902.1 | c.395C>T | p.Pro132Leu | missense_variant | Exon 5 of 20 | ENST00000370709.4 | NP_001368831.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SAGE1 | ENST00000370709.4 | c.395C>T | p.Pro132Leu | missense_variant | Exon 5 of 20 | 5 | NM_001381902.1 | ENSP00000359743.3 | ||
SAGE1 | ENST00000324447.8 | c.395C>T | p.Pro132Leu | missense_variant | Exon 5 of 20 | 5 | ENSP00000323191.3 |
Frequencies
GnomAD3 genomes AF: 0.00000903 AC: 1AN: 110692Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33174
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183176Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67656
GnomAD4 exome AF: 0.00000457 AC: 5AN: 1095151Hom.: 0 Cov.: 28 AF XY: 0.00000555 AC XY: 2AN XY: 360661
GnomAD4 genome AF: 0.00000903 AC: 1AN: 110692Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33174
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.395C>T (p.P132L) alteration is located in exon 5 (coding exon 4) of the SAGE1 gene. This alteration results from a C to T substitution at nucleotide position 395, causing the proline (P) at amino acid position 132 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at