chr17-7294475-C-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015982.4(YBX2):c.26G>T(p.Gly9Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 1,471,966 control chromosomes in the GnomAD database, including 461,692 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_015982.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
YBX2 | NM_015982.4 | c.26G>T | p.Gly9Val | missense_variant | 1/9 | ENST00000007699.10 | NP_057066.2 | |
YBX2 | XM_017024713.3 | c.26G>T | p.Gly9Val | missense_variant | 1/10 | XP_016880202.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
YBX2 | ENST00000007699.10 | c.26G>T | p.Gly9Val | missense_variant | 1/9 | 1 | NM_015982.4 | ENSP00000007699.5 | ||
YBX2 | ENST00000571127.1 | n.82G>T | non_coding_transcript_exon_variant | 1/2 | 2 | |||||
YBX2 | ENST00000571485.5 | n.115G>T | non_coding_transcript_exon_variant | 1/6 | 2 | |||||
YBX2 | ENST00000570627.1 | n.48+93G>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.797 AC: 120305AN: 151030Hom.: 48138 Cov.: 33
GnomAD3 exomes AF: 0.725 AC: 64248AN: 88634Hom.: 23871 AF XY: 0.727 AC XY: 36387AN XY: 50060
GnomAD4 exome AF: 0.789 AC: 1042475AN: 1320828Hom.: 413490 Cov.: 72 AF XY: 0.785 AC XY: 511802AN XY: 651606
GnomAD4 genome AF: 0.797 AC: 120424AN: 151138Hom.: 48202 Cov.: 33 AF XY: 0.794 AC XY: 58614AN XY: 73816
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at