19-3178950-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003775.4(S1PR4):c.158C>T(p.Ser53Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000843 in 1,541,760 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003775.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
S1PR4 | ENST00000246115.5 | c.158C>T | p.Ser53Leu | missense_variant | Exon 1 of 1 | 6 | NM_003775.4 | ENSP00000246115.3 | ||
S1PR4 | ENST00000591346.1 | n.100-264C>T | intron_variant | Intron 1 of 1 | 3 | |||||
ENSG00000289471 | ENST00000687895.2 | n.-242G>A | upstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000709 AC: 1AN: 140964Hom.: 0 AF XY: 0.0000127 AC XY: 1AN XY: 78496
GnomAD4 exome AF: 0.00000864 AC: 12AN: 1389598Hom.: 0 Cov.: 32 AF XY: 0.00000728 AC XY: 5AN XY: 686812
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.158C>T (p.S53L) alteration is located in exon 1 (coding exon 1) of the S1PR4 gene. This alteration results from a C to T substitution at nucleotide position 158, causing the serine (S) at amino acid position 53 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