chr9-127890659-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_013443.5(ST6GALNAC6):c.682C>T(p.Arg228Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000428 in 1,613,266 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. R228Q) has been classified 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ST6GALNAC6 | NM_013443.5 | c.682C>T | p.Arg228Trp | missense_variant | 5/7 | ENST00000373146.6 | |
ST6GALNAC4-ST6GALNAC6-AK1 | NR_174625.1 | n.1558C>T | non_coding_transcript_exon_variant | 7/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST6GALNAC6 | ENST00000373146.6 | c.682C>T | p.Arg228Trp | missense_variant | 5/7 | 1 | NM_013443.5 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152250Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000483 AC: 12AN: 248302Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134842
GnomAD4 exome AF: 0.0000424 AC: 62AN: 1460898Hom.: 0 Cov.: 32 AF XY: 0.0000385 AC XY: 28AN XY: 726752
GnomAD4 genome AF: 0.0000459 AC: 7AN: 152368Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74516
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.682C>T (p.R228W) alteration is located in exon 5 (coding exon 4) of the ST6GALNAC6 gene. This alteration results from a C to T substitution at nucleotide position 682, causing the arginine (R) at amino acid position 228 to be replaced by a tryptophan (W). 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