11-45649762-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003654.6(CHST1):c.1162G>A(p.Ala388Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000621 in 1,610,694 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_003654.6 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 |
---|---|---|---|---|---|---|---|---|
CHST1 | NM_003654.6 | c.1162G>A | p.Ala388Thr | missense_variant | Exon 4 of 4 | ENST00000308064.7 | NP_003645.1 | |
CHST1 | XM_006718356.5 | c.1162G>A | p.Ala388Thr | missense_variant | Exon 4 of 5 | XP_006718419.1 | ||
CHST1 | XM_017018459.3 | c.1162G>A | p.Ala388Thr | missense_variant | Exon 4 of 5 | XP_016873948.1 | ||
CHST1 | XM_047427781.1 | c.1162G>A | p.Ala388Thr | missense_variant | Exon 4 of 4 | XP_047283737.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248698Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134814
GnomAD4 exome AF: 0.00000549 AC: 8AN: 1458468Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2AN XY: 725588
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1162G>A (p.A388T) alteration is located in exon 1 (coding exon 1) of the CHST1 gene. This alteration results from a G to A substitution at nucleotide position 1162, causing the alanine (A) at amino acid position 388 to be replaced by a threonine (T). 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