X-100914769-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_212559.3(XKRX):c.919G>A(p.Gly307Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000107 in 1,209,530 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. In-silico tool predicts a pathogenic 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
XKRX | NM_212559.3 | c.919G>A | p.Gly307Ser | missense_variant | Exon 3 of 3 | ENST00000372956.3 | NP_997724.2 | |
XKRX | XM_011530954.4 | c.958G>A | p.Gly320Ser | missense_variant | Exon 3 of 4 | XP_011529256.1 | ||
XKRX | XM_011530955.2 | c.571G>A | p.Gly191Ser | missense_variant | Exon 4 of 4 | XP_011529257.1 | ||
XKRX | XM_017029517.2 | c.307G>A | p.Gly103Ser | missense_variant | Exon 2 of 2 | XP_016885006.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000270 AC: 3AN: 111264Hom.: 0 Cov.: 23 AF XY: 0.0000897 AC XY: 3AN XY: 33460
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183379Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67843
GnomAD4 exome AF: 0.00000911 AC: 10AN: 1098213Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 5AN XY: 363569
GnomAD4 genome AF: 0.0000270 AC: 3AN: 111317Hom.: 0 Cov.: 23 AF XY: 0.0000895 AC XY: 3AN XY: 33523
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.919G>A (p.G307S) 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 919, causing the glycine (G) at amino acid position 307 to be replaced by a serine (S). 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