12-104757230-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018413.6(CHST11):āc.486G>Cā(p.Lys162Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000159 in 1,614,020 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 ).
Frequency
Consequence
NM_018413.6 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHST11 | NM_018413.6 | c.486G>C | p.Lys162Asn | missense_variant | Exon 3 of 3 | ENST00000303694.6 | NP_060883.1 | |
CHST11 | NM_001173982.2 | c.471G>C | p.Lys157Asn | missense_variant | Exon 3 of 3 | NP_001167453.1 | ||
CHST11 | XM_047428914.1 | c.249G>C | p.Lys83Asn | missense_variant | Exon 2 of 2 | XP_047284870.1 | ||
CHST11 | XM_047428915.1 | c.249G>C | p.Lys83Asn | missense_variant | Exon 2 of 2 | XP_047284871.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHST11 | ENST00000303694.6 | c.486G>C | p.Lys162Asn | missense_variant | Exon 3 of 3 | 1 | NM_018413.6 | ENSP00000305725.5 | ||
CHST11 | ENST00000549260.5 | c.471G>C | p.Lys157Asn | missense_variant | Exon 3 of 3 | 1 | ENSP00000450004.1 | |||
CHST11 | ENST00000549016.1 | c.366G>C | p.Lys122Asn | missense_variant | Exon 3 of 3 | 4 | ENSP00000449095.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000915 AC: 23AN: 251392Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135902
GnomAD4 exome AF: 0.000170 AC: 248AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.000169 AC XY: 123AN XY: 727242
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.486G>C (p.K162N) alteration is located in exon 3 (coding exon 3) of the CHST11 gene. This alteration results from a G to C substitution at nucleotide position 486, causing the lysine (K) at amino acid position 162 to be replaced by an asparagine (N). 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