18-46680461-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_013305.6(ST8SIA5):c.712G>T(p.Val238Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,454,992 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_013305.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ST8SIA5 | NM_013305.6 | c.712G>T | p.Val238Leu | missense_variant | 7/7 | ENST00000315087.12 | NP_037437.2 | |
ST8SIA5 | NM_001307986.2 | c.820G>T | p.Val274Leu | missense_variant | 8/8 | NP_001294915.1 | ||
ST8SIA5 | NM_001307987.2 | c.619G>T | p.Val207Leu | missense_variant | 6/6 | NP_001294916.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ST8SIA5 | ENST00000315087.12 | c.712G>T | p.Val238Leu | missense_variant | 7/7 | 1 | NM_013305.6 | ENSP00000321343 | P4 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000421 AC: 1AN: 237272Hom.: 0 AF XY: 0.00000775 AC XY: 1AN XY: 128978
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1454992Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2AN XY: 723348
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 01, 2022 | The c.712G>T (p.V238L) alteration is located in exon 7 (coding exon 7) of the ST8SIA5 gene. This alteration results from a G to T substitution at nucleotide position 712, causing the valine (V) at amino acid position 238 to be replaced by a leucine (L). 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