8-70681069-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001011720.2(XKR9):c.11C>G(p.Thr4Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000559 in 1,610,714 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001011720.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152012Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249528Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134946
GnomAD4 exome AF: 0.00000480 AC: 7AN: 1458702Hom.: 0 Cov.: 30 AF XY: 0.00000414 AC XY: 3AN XY: 725476
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152012Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74230
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.11C>G (p.T4S) alteration is located in exon 3 (coding exon 1) of the XKR9 gene. This alteration results from a C to G substitution at nucleotide position 11, causing the threonine (T) at amino acid position 4 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