rs758711603
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_173216.2(ST6GAL1):c.748A>C(p.Asn250His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000489 in 1,613,950 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 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. N250S) has been classified as Uncertain significance.
Frequency
Consequence
NM_173216.2 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ST6GAL1 | NM_173216.2 | c.748A>C | p.Asn250His | missense_variant | Exon 6 of 8 | ENST00000169298.8 | NP_775323.1 | |
ST6GAL1 | NM_001353916.2 | c.748A>C | p.Asn250His | missense_variant | Exon 4 of 6 | NP_001340845.1 | ||
ST6GAL1 | NM_003032.3 | c.748A>C | p.Asn250His | missense_variant | Exon 5 of 7 | NP_003023.1 | ||
ST6GAL1 | NM_173217.2 | c.55A>C | p.Asn19His | missense_variant | Exon 5 of 7 | NP_775324.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152180Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000636 AC: 16AN: 251488 AF XY: 0.0000368 show subpopulations
GnomAD4 exome AF: 0.0000506 AC: 74AN: 1461770Hom.: 0 Cov.: 30 AF XY: 0.0000468 AC XY: 34AN XY: 727186 show subpopulations
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74350 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.748A>C (p.N250H) alteration is located in exon 6 (coding exon 3) of the ST6GAL1 gene. This alteration results from a A to C substitution at nucleotide position 748, causing the asparagine (N) at amino acid position 250 to be replaced by a histidine (H). 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