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HTRA1
Final classification
VUS
HTRA1 c.333G>A · p.Val111=
HTRA1

NM_002775.4:c.333G>A (p.Val111=) is a synonymous variant in exon 1 of HTRA1, encoding HtrA serine peptidase 1.

Gene
HTRA1
Transcript
NM_002775.4
HGVS · transcript:coding
NM_002775.4:c.333G>A
Consequence
N/A
GRCh38
chr10:122461985 G>A
GRCh37
chr10:124221501 G>A
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP4 supporting benign, BP7 supporting benign; combination = 1 supporting + 2 supporting benign, which maps to VUS because the evidence is conflicting.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP4 supporting benign, BP7 supporting benign; combination = 1 supporting + 2 supporting benign, which maps to VUS because the evidence is conflicting.
Classification rationale
PM2 BP4BP7 VUS
HTRA1 c.333G>A

NM_002775.4:c.333G>A (p.Val111=) is a synonymous variant in exon 1 of HTRA1, encoding HtrA serine peptidase 1. This variant is ultra-rare in population databases: absent from gnomAD v2.1 and present in gnomAD v4.1 at an allele frequency of 6.56e-7 (1/1,524,404 alleles), satisfying PM2 at supporting strength.1 Computational evidence supports a benign interpretation: REVEL score is 0.041 (well below the 0.5 pathogenic threshold), and SpliceAI predicts no splicing alteration (max delta = 0.00), meeting BP4 at supporting benign strength.2 As a synonymous variant with no predicted splicing impact (SpliceAI max delta = 0.00) and low nucleotide conservation (REVEL = 0.041), this variant meets BP7 at supporting benign strength.3 No functional studies, segregation data, de novo observations, case-control analyses, ClinVar classifications, or variant-specific publications are available for this variant. All other ACMG/AMP criteria are either not met or not applicable. The evidence profile is conflicting: PM2_Supporting on the pathogenic side versus BP4_Supporting and BP7_Supporting on the benign side. Per the generic ACMG/AMP 2015 final classification rules (PMID:25741868), this constellation of conflicting supporting-level evidence is insufficient to reach a Likely Benign or Likely Pathogenic classification. The variant is classified as a Variant of Uncertain Significance (VUS).4

PM2 + BP4 + BP7 VUS
2 revelspliceai ↗
3 spliceai ↗revel
4 generic_acmg_combination_rules
Gene diagram · NM_002775.4 · variants mapped to exon structure
HTRA1 NM_002775.4
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 17 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
PM2 (absent or extremely low frequency in population databases) is met at supporting strength. NM_002775.4:c.333G>A is absent from gnomAD v2.1 and is present in gnomAD v4.1 at an allele frequency of 6.56e-7 (1/1,524,404 alleles), well below the generic ACMG PM2 threshold of 0.1%. It is also absent from gnomAD-Canada v1.0.
Absent from gnomAD v2.1gnomAD v4.1 total AF=6.56e-7 (1/1524
BP4 supporting Benign
BP4 (multiple lines of computational evidence suggest no impact on gene product) is met at supporting benign strength. REVEL score is 0.041, strongly favoring a benign interpretation (typical pathogenic threshold >0.5). SpliceAI max delta score is 0.00, predicting no splicing alteration. Together these indicate no computational evidence of a deleterious effect.
REVEL=0.041 (benignfar below 0.5 threshold)SpliceAI max delta=0.00 (no splicing impact).
BP7 supporting Benign
BP7 (synonymous variant with no predicted splicing impact and nucleotide not highly conserved) is met at supporting benign strength. NM_002775.4:c.333G>A is a synonymous variant (p.Val111=). SpliceAI predicts no splicing alteration (max delta = 0.00). The low REVEL score (0.041) indicates the nucleotide position is not highly conserved across species.
Synonymous variant p.(Val111=)SpliceAI max delta=0.00 (no splice impact)REVEL=0.041 (nucleotide not conserved).
Assessed · not applied
Pathogenic
PS2 PS2 (de novo with confirmed paternity/maternity) is not met.
PS3 PS3 (well-established functional studies supporting a damaging effect) is not met.
PS4 PS4 (prevalence in affected individuals significantly increased compared to controls) is not met.
PM1 PM1 (located in a mutational hot spot or critical functional domain) is not met.
PM6 PM6 (de novo without confirmation of paternity/maternity) is not met.
PP1 PP1 (cosegregation with disease in multiple affected family members) is not met.
PP3 PP3 (multiple lines of computational evidence support a deleterious effect) is not met.
PP4 PP4 (patient phenotype or family history highly specific for the gene) is not met.
PP5 PP5 (reputable source reports variant as pathogenic) is not met.
Benign
BA1 BA1 (allele frequency >1% in any population) is not met.
BS1 BS1 (allele frequency greater than expected for the disorder) is not met.
BS2 BS2 (observed in a healthy adult individual in the homozygous state, or hemizygous in a male for an X-linked gene with full penetrance expected at an early age) is not met.
BS3 BS3 (well-established functional studies show no damaging effect) is not met.
BS4 BS4 (lack of segregation with disease in affected family members) is not met.
BP2 BP2 (observed in trans with a pathogenic variant for a dominant disorder, or in cis with a pathogenic variant) is not met.
BP5 BP5 (variant found in a case with an alternate molecular basis for disease) is not met.
BP6 BP6 (reputable source reports variant as benign) is not met.
N/A · 5 PVS1 · PS1 · PM5 · PP2 · BP1
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 6.55994e-07; MAF= 0.00007%, 1/1524404 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 1.97871e-05; MAF= 0.00198%, 1/50538 alleles, homozygotes = 0).
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
This variant is absent from gnomAD-Canada.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
6.6e-05% · 1 / 1,524,404
0 hom
Admixed American
1 / 50,538
0.002%
+ 9 not observed (Remaining individuals, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.041.
Functional No data
No calibrated functional assay or RNA evidence was identified for this variant.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
7Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
SpliceAI
OncoKB
COSMIC
Cancer hotspots