chr15-40471343-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_130468.4(CHST14):c.130A>G(p.Met44Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000194 in 1,548,420 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_130468.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHST14 | NM_130468.4 | c.130A>G | p.Met44Val | missense_variant | 1/1 | ENST00000306243.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHST14 | ENST00000306243.7 | c.130A>G | p.Met44Val | missense_variant | 1/1 | NM_130468.4 | P1 | ||
CHST14 | ENST00000559991.1 | c.130A>G | p.Met44Val | missense_variant | 1/2 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152004Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000133 AC: 2AN: 150884Hom.: 0 AF XY: 0.0000244 AC XY: 2AN XY: 82050
GnomAD4 exome AF: 0.00000143 AC: 2AN: 1396416Hom.: 0 Cov.: 32 AF XY: 0.00000145 AC XY: 1AN XY: 690234
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152004Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74224
ClinVar
Submissions by phenotype
Ehlers-Danlos syndrome, musculocontractural type Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Apr 27, 2018 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with CHST14-related disease. This sequence change replaces methionine with valine at codon 44 of the CHST14 protein (p.Met44Val). The methionine residue is moderately conserved and there is a small physicochemical difference between methionine and valine. While this variant is not present in population databases, the frequency information is unreliable, as metrics indicate poor data quality at this position in the ExAC database. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at