chr13-33016484-C-CGTCGCT
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_004795.4(KL):c.52_57dupTCGCTG(p.Ser18_Leu19dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000126 in 1,162,530 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004795.4 conservative_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KL | ENST00000380099.4 | c.52_57dupTCGCTG | p.Ser18_Leu19dup | conservative_inframe_insertion | Exon 1 of 5 | 1 | NM_004795.4 | ENSP00000369442.3 | ||
KL | ENST00000487852.1 | n.60_65dupTCGCTG | non_coding_transcript_exon_variant | Exon 1 of 5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000163 AC: 24AN: 147332Hom.: 0 Cov.: 30
GnomAD4 exome AF: 0.000120 AC: 122AN: 1015198Hom.: 1 Cov.: 28 AF XY: 0.000121 AC XY: 58AN XY: 478594
GnomAD4 genome AF: 0.000163 AC: 24AN: 147332Hom.: 0 Cov.: 30 AF XY: 0.000153 AC XY: 11AN XY: 71684
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant, c.52_57dup, results in the insertion of 2 amino acid(s) of the KL protein (p.Ser18_Leu19dup), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with KL-related conditions. 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at