12-104757268-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_018413.6(CHST11):c.524G>A(p.Arg175His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000176 in 1,614,066 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018413.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHST11 | NM_018413.6 | c.524G>A | p.Arg175His | missense_variant | Exon 3 of 3 | ENST00000303694.6 | NP_060883.1 | |
CHST11 | NM_001173982.2 | c.509G>A | p.Arg170His | missense_variant | Exon 3 of 3 | NP_001167453.1 | ||
CHST11 | XM_047428914.1 | c.287G>A | p.Arg96His | missense_variant | Exon 2 of 2 | XP_047284870.1 | ||
CHST11 | XM_047428915.1 | c.287G>A | p.Arg96His | 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.524G>A | p.Arg175His | missense_variant | Exon 3 of 3 | 1 | NM_018413.6 | ENSP00000305725.5 | ||
CHST11 | ENST00000549260.5 | c.509G>A | p.Arg170His | missense_variant | Exon 3 of 3 | 1 | ENSP00000450004.1 | |||
CHST11 | ENST00000549016.1 | c.404G>A | p.Arg135His | missense_variant | Exon 3 of 3 | 4 | ENSP00000449095.1 |
Frequencies
GnomAD3 genomes AF: 0.0000921 AC: 14AN: 152072Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000215 AC: 54AN: 251422Hom.: 1 AF XY: 0.000287 AC XY: 39AN XY: 135890
GnomAD4 exome AF: 0.000185 AC: 270AN: 1461876Hom.: 2 Cov.: 31 AF XY: 0.000242 AC XY: 176AN XY: 727240
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74414
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.524G>A (p.R175H) alteration is located in exon 3 (coding exon 3) of the CHST11 gene. This alteration results from a G to A substitution at nucleotide position 524, causing the arginine (R) at amino acid position 175 to be replaced by a histidine (H). 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