12-104457440-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018413.6(CHST11):c.29G>A(p.Arg10Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,614,010 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 (★).
Frequency
Consequence
NM_018413.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.29G>A | p.Arg10Lys | missense_variant | Exon 1 of 3 | ENST00000303694.6 | NP_060883.1 | |
CHST11 | NM_001173982.2 | c.29G>A | p.Arg10Lys | missense_variant | Exon 1 of 3 | NP_001167453.1 | ||
CHST11 | XM_047428914.1 | c.-123G>A | 5_prime_UTR_variant | Exon 1 of 2 | XP_047284870.1 | |||
CHST11 | XM_047428915.1 | c.-108G>A | 5_prime_UTR_variant | Exon 1 of 2 | XP_047284871.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHST11 | ENST00000303694.6 | c.29G>A | p.Arg10Lys | missense_variant | Exon 1 of 3 | 1 | NM_018413.6 | ENSP00000305725.5 | ||
CHST11 | ENST00000549260.5 | c.29G>A | p.Arg10Lys | missense_variant | Exon 1 of 3 | 1 | ENSP00000450004.1 | |||
CHST11 | ENST00000547956.1 | c.29G>A | p.Arg10Lys | missense_variant | Exon 1 of 2 | 2 | ENSP00000449093.1 | |||
CHST11 | ENST00000546689.1 | c.29G>A | p.Arg10Lys | missense_variant | Exon 1 of 2 | 2 | ENSP00000448678.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251322Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135854
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461756Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727196
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.29G>A (p.R10K) alteration is located in exon 1 (coding exon 1) of the CHST11 gene. This alteration results from a G to A substitution at nucleotide position 29, causing the arginine (R) at amino acid position 10 to be replaced by a lysine (K). 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