chr5-100856292-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005668.6(ST8SIA4):c.608G>A(p.Arg203Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000446 in 1,613,920 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005668.6 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 |
---|---|---|---|---|---|---|---|
ST8SIA4 | NM_005668.6 | c.608G>A | p.Arg203Gln | missense_variant | 4/5 | ENST00000231461.10 | |
ST8SIA4 | XM_005272078.4 | c.608G>A | p.Arg203Gln | missense_variant | 4/5 | ||
ST8SIA4 | XM_011543630.3 | c.503+30051G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST8SIA4 | ENST00000231461.10 | c.608G>A | p.Arg203Gln | missense_variant | 4/5 | 1 | NM_005668.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000717 AC: 18AN: 251146Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135734
GnomAD4 exome AF: 0.0000438 AC: 64AN: 1461808Hom.: 0 Cov.: 31 AF XY: 0.0000399 AC XY: 29AN XY: 727204
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 16, 2021 | The c.608G>A (p.R203Q) alteration is located in exon 4 (coding exon 4) of the ST8SIA4 gene. This alteration results from a G to A substitution at nucleotide position 608, causing the arginine (R) at amino acid position 203 to be replaced by a glutamine (Q). 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