10-122461681-CGCTGCT-CGCTGCTGCTGCTGCT
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4
The NM_002775.5(HTRA1):c.40_48dupCTGCTGCTG(p.Leu14_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 0.00000862 in 1,159,658 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000086 ( 0 hom. )
Consequence
HTRA1
NM_002775.5 conservative_inframe_insertion
NM_002775.5 conservative_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0930
Genes affected
HTRA1 (HGNC:9476): (HtrA serine peptidase 1) This gene encodes a member of the trypsin family of serine proteases. This protein is a secreted enzyme that is proposed to regulate the availability of insulin-like growth factors (IGFs) by cleaving IGF-binding proteins. It has also been suggested to be a regulator of cell growth. Variations in the promoter region of this gene are the cause of susceptibility to age-related macular degeneration type 7. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_002775.5.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HTRA1 | ENST00000368984.8 | c.40_48dupCTGCTGCTG | p.Leu14_Leu16dup | conservative_inframe_insertion | Exon 1 of 9 | 1 | NM_002775.5 | ENSP00000357980.3 | ||
HTRA1 | ENST00000648167.1 | c.154+2983_154+2991dupCTGCTGCTG | intron_variant | Intron 1 of 8 | ENSP00000498033.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000862 AC: 10AN: 1159658Hom.: 0 Cov.: 30 AF XY: 0.00000701 AC XY: 4AN XY: 571006
GnomAD4 exome
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10
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1159658
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30
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4
AN XY:
571006
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
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Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at