chr10-122461681-C-CGCT
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PM4_SupportingBS1_Supporting
The NM_002775.5(HTRA1):c.46_48dupCTG(p.Leu16dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000987 in 1,307,156 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_002775.5 conservative_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HTRA1 | ENST00000368984.8 | c.46_48dupCTG | p.Leu16dup | conservative_inframe_insertion | Exon 1 of 9 | 1 | NM_002775.5 | ENSP00000357980.3 | ||
HTRA1 | ENST00000648167.1 | c.154+2989_154+2991dupCTG | intron_variant | Intron 1 of 8 | ENSP00000498033.1 |
Frequencies
GnomAD3 genomes AF: 0.000393 AC: 58AN: 147452Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000903 AC: 6AN: 66442Hom.: 0 AF XY: 0.0000527 AC XY: 2AN XY: 37970
GnomAD4 exome AF: 0.0000604 AC: 70AN: 1159602Hom.: 0 Cov.: 30 AF XY: 0.0000508 AC XY: 29AN XY: 570978
GnomAD4 genome AF: 0.000400 AC: 59AN: 147554Hom.: 0 Cov.: 32 AF XY: 0.000418 AC XY: 30AN XY: 71842
ClinVar
Submissions by phenotype
not provided Uncertain:2
This variant, c.46_48dup, results in the insertion of 1 amino acid(s) of the HTRA1 protein (p.Leu16dup), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs770388445, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with HTRA1-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. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at