6-144186648-ACTT-A
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 1P and 1B. PM4_SupportingBS1_Supporting
The NM_003764.4(STX11):c.24_26delTCT(p.Leu9del) variant causes a disruptive inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000411 in 1,614,018 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_003764.4 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STX11 | ENST00000367568.5 | c.24_26delTCT | p.Leu9del | disruptive_inframe_deletion | Exon 2 of 2 | 1 | NM_003764.4 | ENSP00000356540.4 | ||
STX11 | ENST00000698355.1 | c.24_26delTCT | p.Leu9del | disruptive_inframe_deletion | Exon 3 of 3 | ENSP00000513678.1 | ||||
STX11 | ENST00000698356.1 | c.24_26delTCT | p.Leu9del | disruptive_inframe_deletion | Exon 4 of 4 | ENSP00000513679.1 | ||||
STX11 | ENST00000698357.1 | c.24_26delTCT | p.Leu9del | disruptive_inframe_deletion | Exon 2 of 2 | ENSP00000513680.1 |
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 42AN: 152214Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.000211 AC: 53AN: 251272 AF XY: 0.000177 show subpopulations
GnomAD4 exome AF: 0.000426 AC: 622AN: 1461804Hom.: 0 AF XY: 0.000407 AC XY: 296AN XY: 727212 show subpopulations
GnomAD4 genome AF: 0.000276 AC: 42AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74370 show subpopulations
ClinVar
Submissions by phenotype
Familial hemophagocytic lymphohistiocytosis 4 Uncertain:1
This variant, c.24_26del, results in the deletion of 1 amino acid(s) of the STX11 protein (p.Leu9del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs760492745, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with STX11-related conditions. ClinVar contains an entry for this variant (Variation ID: 355597). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Familial hemophagocytic lymphohistiocytosis Uncertain:1
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Autoinflammatory syndrome Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at