17-7294347-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015982.4(YBX2):c.154G>A(p.Gly52Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000222 in 1,349,186 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_015982.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
YBX2 | NM_015982.4 | c.154G>A | p.Gly52Ser | missense_variant | 1/9 | ENST00000007699.10 | NP_057066.2 | |
YBX2 | XM_017024713.3 | c.154G>A | p.Gly52Ser | missense_variant | 1/10 | XP_016880202.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
YBX2 | ENST00000007699.10 | c.154G>A | p.Gly52Ser | missense_variant | 1/9 | 1 | NM_015982.4 | ENSP00000007699.5 | ||
YBX2 | ENST00000571127.1 | n.210G>A | non_coding_transcript_exon_variant | 1/2 | 2 | |||||
YBX2 | ENST00000571485.5 | n.243G>A | non_coding_transcript_exon_variant | 1/6 | 2 | |||||
YBX2 | ENST00000570627.1 | n.48+221G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151752Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000167 AC: 2AN: 1197434Hom.: 0 Cov.: 62 AF XY: 0.00000171 AC XY: 1AN XY: 585146
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151752Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74112
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 08, 2022 | The c.154G>A (p.G52S) alteration is located in exon 1 (coding exon 1) of the YBX2 gene. This alteration results from a G to A substitution at nucleotide position 154, causing the glycine (G) at amino acid position 52 to be replaced by a serine (S). 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