2-106843848-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001142351.2(ST6GAL2):c.130T>A(p.Ser44Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,912 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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. S44C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001142351.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ST6GAL2 | NM_001142351.2 | c.130T>A | p.Ser44Thr | missense_variant | 2/6 | ENST00000409382.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST6GAL2 | ENST00000409382.8 | c.130T>A | p.Ser44Thr | missense_variant | 2/6 | 1 | NM_001142351.2 | P1 | |
ST6GAL2 | ENST00000361686.8 | c.130T>A | p.Ser44Thr | missense_variant | 2/6 | 1 | P1 | ||
ST6GAL2 | ENST00000409087.3 | c.130T>A | p.Ser44Thr | missense_variant | 2/6 | 1 | |||
ST6GAL2 | ENST00000419159.2 | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459912Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726308
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 05, 2023 | The c.130T>A (p.S44T) alteration is located in exon 2 (coding exon 1) of the ST6GAL2 gene. This alteration results from a T to A substitution at nucleotide position 130, causing the serine (S) at amino acid position 44 to be replaced by a threonine (T). 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
Publications
No publications associated with this variant yet.