9-127890646-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_013443.5(ST6GALNAC6):c.695G>A(p.Gly232Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000118 in 1,613,060 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 (★).
Frequency
Consequence
NM_013443.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ST6GALNAC6 | NM_013443.5 | c.695G>A | p.Gly232Asp | missense_variant | Exon 5 of 7 | ENST00000373146.6 | NP_038471.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ST6GALNAC6 | ENST00000373146.6 | c.695G>A | p.Gly232Asp | missense_variant | Exon 5 of 7 | 1 | NM_013443.5 | ENSP00000362239.1 | ||
ENSG00000257524 | ENST00000646171.1 | n.593G>A | non_coding_transcript_exon_variant | Exon 4 of 13 | ENSP00000495484.1 |
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000404 AC: 10AN: 247372Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134480
GnomAD4 exome AF: 0.000125 AC: 183AN: 1460820Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 78AN XY: 726702
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.695G>A (p.G232D) alteration is located in exon 5 (coding exon 4) of the ST6GALNAC6 gene. This alteration results from a G to A substitution at nucleotide position 695, causing the glycine (G) at amino acid position 232 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