18-46686187-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_013305.6(ST8SIA5):c.556G>A(p.Asp186Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 1,461,860 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013305.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ST8SIA5 | NM_013305.6 | c.556G>A | p.Asp186Asn | missense_variant | Exon 5 of 7 | ENST00000315087.12 | NP_037437.2 | |
ST8SIA5 | NM_001307986.2 | c.664G>A | p.Asp222Asn | missense_variant | Exon 6 of 8 | NP_001294915.1 | ||
ST8SIA5 | NM_001307987.2 | c.463G>A | p.Asp155Asn | missense_variant | Exon 4 of 6 | NP_001294916.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251480Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135918
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461860Hom.: 1 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727234
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.556G>A (p.D186N) alteration is located in exon 5 (coding exon 5) of the ST8SIA5 gene. This alteration results from a G to A substitution at nucleotide position 556, causing the aspartic acid (D) at amino acid position 186 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