chr1-42696753-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_004559.5(YBX1):c.466C>T(p.Arg156Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000116 in 1,461,568 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004559.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
YBX1 | NM_004559.5 | c.466C>T | p.Arg156Cys | missense_variant | Exon 5 of 8 | ENST00000321358.12 | NP_004550.2 | |
YBX1 | XM_047421495.1 | c.376C>T | p.Arg126Cys | missense_variant | Exon 4 of 6 | XP_047277451.1 | ||
YBX1 | NR_132737.2 | n.466C>T | non_coding_transcript_exon_variant | Exon 4 of 7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
YBX1 | ENST00000321358.12 | c.466C>T | p.Arg156Cys | missense_variant | Exon 5 of 8 | 1 | NM_004559.5 | ENSP00000361626.3 | ||
YBX1 | ENST00000436427.1 | c.613C>T | p.Arg205Cys | missense_variant | Exon 4 of 7 | 1 | ENSP00000389639.1 | |||
YBX1 | ENST00000332220.10 | c.376C>T | p.Arg126Cys | missense_variant | Exon 4 of 5 | 5 | ENSP00000405937.1 | |||
YBX1 | ENST00000467957.1 | n.547C>T | non_coding_transcript_exon_variant | Exon 4 of 5 | 2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251080Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135692
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461568Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727096
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.466C>T (p.R156C) alteration is located in exon 5 (coding exon 5) of the YBX1 gene. This alteration results from a C to T substitution at nucleotide position 466, causing the arginine (R) at amino acid position 156 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