chr14-34462156-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_138288.4(SPTSSA):āc.52T>Gā(p.Tyr18Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000261 in 1,531,216 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y18N) has been classified as Uncertain significance.
Frequency
Consequence
NM_138288.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPTSSA | NM_138288.4 | c.52T>G | p.Tyr18Asp | missense_variant | 1/2 | ENST00000298130.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTSSA | ENST00000298130.5 | c.52T>G | p.Tyr18Asp | missense_variant | 1/2 | 1 | NM_138288.4 | P1 | |
EGLN3 | ENST00000551935.5 | n.59+560T>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000133 AC: 2AN: 150142Hom.: 0 Cov.: 29
GnomAD4 exome AF: 0.00000145 AC: 2AN: 1381074Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 687348
GnomAD4 genome AF: 0.0000133 AC: 2AN: 150142Hom.: 0 Cov.: 29 AF XY: 0.0000136 AC XY: 1AN XY: 73268
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 20, 2021 | The c.52T>G (p.Y18D) alteration is located in exon 1 (coding exon 1) of the SPTSSA gene. This alteration results from a T to G substitution at nucleotide position 52, causing the tyrosine (Y) at amino acid position 18 to be replaced by an aspartic acid (D). 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