X-135896274-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001381902.1(SAGE1):c.32C>T(p.Pro11Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000237 in 1,204,401 control chromosomes in the GnomAD database, including 2 homozygotes. There are 91 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001381902.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SAGE1 | NM_001381902.1 | c.32C>T | p.Pro11Leu | missense_variant | Exon 2 of 20 | ENST00000370709.4 | NP_001368831.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000330 AC: 37AN: 112065Hom.: 0 Cov.: 23 AF XY: 0.000380 AC XY: 13AN XY: 34255
GnomAD3 exomes AF: 0.000797 AC: 146AN: 183133Hom.: 1 AF XY: 0.000725 AC XY: 49AN XY: 67607
GnomAD4 exome AF: 0.000228 AC: 249AN: 1092282Hom.: 2 Cov.: 27 AF XY: 0.000218 AC XY: 78AN XY: 358598
GnomAD4 genome AF: 0.000330 AC: 37AN: 112119Hom.: 0 Cov.: 23 AF XY: 0.000379 AC XY: 13AN XY: 34319
ClinVar
Submissions by phenotype
SAGE1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at