17-7289610-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015982.4(YBX2):c.964C>T(p.Arg322Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,613,590 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R322H) has been classified 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YBX2 | NM_015982.4 | c.964C>T | p.Arg322Cys | missense_variant | 7/9 | ENST00000007699.10 | |
YBX2 | XM_017024713.3 | c.1009C>T | p.Arg337Cys | missense_variant | 8/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YBX2 | ENST00000007699.10 | c.964C>T | p.Arg322Cys | missense_variant | 7/9 | 1 | NM_015982.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152028Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000817 AC: 2AN: 244666Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 132892
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461562Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727110
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152028Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74260
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | The c.964C>T (p.R322C) alteration is located in exon 7 (coding exon 7) of the YBX2 gene. This alteration results from a C to T substitution at nucleotide position 964, causing the arginine (R) at amino acid position 322 to be replaced by a cysteine (C). 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