X-135905354-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.416C>T(p.Ala139Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000913 in 1,095,589 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 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 (★).
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.416C>T | p.Ala139Val | 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.416C>T | p.Ala139Val | missense_variant | Exon 5 of 20 | 5 | NM_001381902.1 | ENSP00000359743.3 | ||
SAGE1 | ENST00000324447.8 | c.416C>T | p.Ala139Val | missense_variant | Exon 5 of 20 | 5 | ENSP00000323191.3 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome AF: 0.00000913 AC: 10AN: 1095589Hom.: 0 Cov.: 28 AF XY: 0.0000166 AC XY: 6AN XY: 361067
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.416C>T (p.A139V) 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 416, causing the alanine (A) at amino acid position 139 to be replaced by a valine (V). 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