chr3-187042772-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_173216.2(ST6GAL1):āc.69C>Gā(p.Ile23Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000539 in 1,614,040 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I23T) has been classified as Uncertain significance.
Frequency
Consequence
NM_173216.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ST6GAL1 | NM_173216.2 | c.69C>G | p.Ile23Met | missense_variant | 4/8 | ENST00000169298.8 | |
ST6GAL1 | NM_001353916.2 | c.69C>G | p.Ile23Met | missense_variant | 2/6 | ||
ST6GAL1 | NM_003032.3 | c.69C>G | p.Ile23Met | missense_variant | 3/7 | ||
ST6GAL1 | NM_173217.2 | c.-87+3899C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST6GAL1 | ENST00000169298.8 | c.69C>G | p.Ile23Met | missense_variant | 4/8 | 1 | NM_173216.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251138Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135702
GnomAD4 exome AF: 0.0000581 AC: 85AN: 1461880Hom.: 0 Cov.: 31 AF XY: 0.0000523 AC XY: 38AN XY: 727242
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.69C>G (p.I23M) alteration is located in exon 4 (coding exon 1) of the ST6GAL1 gene. This alteration results from a C to G substitution at nucleotide position 69, causing the isoleucine (I) at amino acid position 23 to be replaced by a methionine (M). 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