17-76625365-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018414.5(ST6GALNAC1):c.1768C>A(p.Arg590Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,613,756 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R590H) has been classified as Uncertain significance.
Frequency
Consequence
NM_018414.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ST6GALNAC1 | NM_018414.5 | c.1768C>A | p.Arg590Ser | missense_variant | 9/9 | ENST00000156626.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST6GALNAC1 | ENST00000156626.12 | c.1768C>A | p.Arg590Ser | missense_variant | 9/9 | 1 | NM_018414.5 | P1 | |
SNHG16 | ENST00000701062.1 | n.282+11360G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000195 AC: 49AN: 251312Hom.: 0 AF XY: 0.000221 AC XY: 30AN XY: 135856
GnomAD4 exome AF: 0.000109 AC: 160AN: 1461546Hom.: 0 Cov.: 32 AF XY: 0.000120 AC XY: 87AN XY: 727054
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2022 | The c.1768C>A (p.R590S) alteration is located in exon 9 (coding exon 9) of the ST6GALNAC1 gene. This alteration results from a C to A substitution at nucleotide position 1768, causing the arginine (R) at amino acid position 590 to be replaced by a serine (S). 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