Back
LYFE SCIENCES
Project: HERA
NM_006767.4:c.2219+13C>T
p.?  ·  LZTR1
Starting
Initialising…
0%
Legacy Engine
Ready
View Legacy →
Classification rationale
1

The LZTR1 c.2219+13C>T (p.?) variant has been reported in ClinVar predominantly as benign, with 8 benign and 1 likely benign clinical laboratory submissions.

clinvar ↗
2

This variant is common in population databases, with gnomAD v2.1 grpmax filtering allele frequency 1.37781% and gnomAD v4.1 grpmax filtering allele frequency 1.43127%, both well above the LZTR1 benign thresholds for BS1 (0.025%) and BA1 (0.05%).

gnomad_v2 ↗ gnomad_v4 ↗ cspec ↗
3

SpliceAI predicts no significant splice impact for this variant, with a maximum delta score of 0.13, which is consistent with BP4 and BP7 rather than a deleterious splicing effect.

spliceai ↗ cspec ↗
Applied criteria
Met
Not met
Not assessed
N/A
Very strong
Strong
Moderate
Supporting
Pathogenic evidence
PVS
PVS1
PS
PS1
PS2
PS3
PS4
PM
PM1
PM2
PM3
PM4
PM5
PM6
PP
PP1
PP2
PP3
PP4
PP5
Benign evidence
BA
BA1
BS
BS1
BS2
BS3
BS4
BP
BP1
BP2
BP3
BP4
BP5
BP6
BP7
PVS1
—
—
Rationale
Select a criterion to inspect its explanation.
Evidence used
  • —
Gaps remaining
  • —
Rule
—
Publications
—
Research and evidence
gnomAD v2.1 evidence
v2.1
gnomAD v4.1 evidence
v4.1
01
Population
gnomAD v2.1This variant is present in gnomAD v2.1 (AF= 0.0100413; MAF= 1.00413%, 2808/279646 alleles, homozygotes = 21) and has highest observed frequency in the European (non-Finnish) population (AF= 0.0142263; MAF= 1.42263%, 1819/127862 alleles, homozygotes = 13); grpmax FAF= 0.0137781.
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 0.0124482; MAF= 1.24482%, 20042/1610034 alleles, homozygotes = 145) and has highest observed frequency in the European (non-Finnish) population (AF= 0.0144949; MAF= 1.44949%, 17089/1178968 alleles, homozygotes = 127); grpmax FAF= 0.0143127.
gnomAD v2 ↗ gnomAD v4 ↗
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Benign (8 clinical laboratories) and as Likely benign (1 clinical laboratory).
ClinVar ↗
03
Functional
No functional summary recorded.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.13).
SpliceAI ↗
COSMIC evidence
05
COSMIC
This variant has previously been reported in somatic cancers (COSMIC; COSV104394247, n = 4 times).
COSMIC ↗
06
Cancer hotspots
No cancer hotspot summary recorded.