chrX-139956185-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001013403.3(CXorf66):c.797G>A(p.Cys266Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000141 in 1,209,716 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001013403.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000268 AC: 3AN: 112011Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34177
GnomAD4 exome AF: 0.0000128 AC: 14AN: 1097705Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 6AN XY: 363063
GnomAD4 genome AF: 0.0000268 AC: 3AN: 112011Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34177
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.797G>A (p.C266Y) alteration is located in exon 3 (coding exon 3) of the CXorf66 gene. This alteration results from a G to A substitution at nucleotide position 797, causing the cysteine (C) at amino acid position 266 to be replaced by a tyrosine (Y). 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