5-100895729-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.170G>A(p.Arg57Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000217 in 1,612,638 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
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 | UniProt |
---|---|---|---|---|---|---|---|
ST8SIA4 | NM_005668.6 | c.170G>A | p.Arg57Gln | missense_variant | 2/5 | ENST00000231461.10 | |
ST8SIA4 | NM_175052.3 | c.170G>A | p.Arg57Gln | missense_variant | 2/3 | ||
ST8SIA4 | XM_005272078.4 | c.170G>A | p.Arg57Gln | missense_variant | 2/5 | ||
ST8SIA4 | XM_011543630.3 | c.170G>A | p.Arg57Gln | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST8SIA4 | ENST00000231461.10 | c.170G>A | p.Arg57Gln | missense_variant | 2/5 | 1 | NM_005668.6 | P1 | |
ST8SIA4 | ENST00000451528.2 | c.170G>A | p.Arg57Gln | missense_variant | 2/3 | 1 | |||
ST8SIA4 | ENST00000523381.1 | c.*178G>A | 3_prime_UTR_variant, NMD_transcript_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151942Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000104 AC: 26AN: 250942Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135636
GnomAD4 exome AF: 0.000236 AC: 345AN: 1460696Hom.: 0 Cov.: 31 AF XY: 0.000184 AC XY: 134AN XY: 726654
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151942Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74218
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.170G>A (p.R57Q) alteration is located in exon 2 (coding exon 2) of the ST8SIA4 gene. This alteration results from a G to A substitution at nucleotide position 170, causing the arginine (R) at amino acid position 57 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