chrX-100914880-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_212559.3(XKRX):c.808G>A(p.Val270Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000082 in 1,098,221 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_212559.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
XKRX | NM_212559.3 | c.808G>A | p.Val270Met | missense_variant | Exon 3 of 3 | ENST00000372956.3 | NP_997724.2 | |
XKRX | XM_011530954.4 | c.847G>A | p.Val283Met | missense_variant | Exon 3 of 4 | XP_011529256.1 | ||
XKRX | XM_011530955.2 | c.460G>A | p.Val154Met | missense_variant | Exon 4 of 4 | XP_011529257.1 | ||
XKRX | XM_017029517.2 | c.196G>A | p.Val66Met | missense_variant | Exon 2 of 2 | XP_016885006.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome AF: 0.00000820 AC: 9AN: 1098221Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 3AN XY: 363575
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.808G>A (p.V270M) alteration is located in exon 3 (coding exon 3) of the XKRX gene. This alteration results from a G to A substitution at nucleotide position 808, causing the valine (V) at amino acid position 270 to be replaced by a methionine (M). 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
Publications
No publications associated with this variant yet.