About DDX41
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
DDX41 c.299-3C>T, p.?
Classification
Not classified
Variant description:
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. Select a step to read what it means.
Not classified yet.Select a step to read what it means.
In plain language
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.
LYFE Sciences is an AI system, and it can make mistakes.
Criteria may be applied incorrectly, sources may be misread, and a
confident-looking classification can still be wrong.
Double-check every criterion and its underlying evidence
before relying on any call.
01The reasoning
How it was classified
The recorded framework is ClinGen DDX41 VCEP v1.0.0. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
Recorded applied criteria
The applied criteria and their strengths are shown as assessed under the stated framework.
Pathogenic evidence criteria: 0
Benign evidence criteria: 0
Pathogenic criteria applied · 0
No pathogenic criterion marked as applied in the recorded assessment.
Benign criteria applied · 0
No benign criterion marked as applied in the recorded assessment.
Recorded classification: Not classified
In progress — classification not generated yet.
02The sources
Evidence at a glance
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1
gnomAD v2.1
Population frequency
20 / 1,614,118 alleles
gnomAD v4.1: 20 / 1,614,118 alleles. Recorded AF 1.23907e-05. Recorded homozygote count 0.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 1.19311e-05; MAF= 0.00119%, 3/251444 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 2.89084e-05; MAF= 0.00289%, 1/34592 alleles, homozygotes = 0); grpmax FAF= 2.92e-06.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
No listed criterion applied
SpliceAI score
0.000 maximum delta
Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.
No listed criterion applied
SpliceAI ↗
ClinVar submissions
3 reported laboratory submissions
3 Uncertain significance. ClinVar API review status: criteria provided, multiple submitters, no conflicts.
Context only
ClinVar ↗
No screenshot for this evidence
Functional evidence
Statement recorded
In progress — evidence not uploaded yet.
No listed criterion applied
OncoKB ↗
Somatic evidence
No matching record reported
This variant has not previously been reported in somatic cancers (COSMIC).
Context only
COSMIC ↗
For specialists
Technical detail
ACMG/AMP criteria under ClinGen DDX41 VCEP v1.0.0, with the data and sources behind each one.
28 criteria with recorded statuses: 0 met · 0 not met · 28 not assessed · 0 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
No criteria match.
Not assessed · 28 · no assessment recorded
PVS1 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
PS1 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
PS2 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
PS3 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
PS4 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
PM1 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
PM2 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
PM3 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
PM4 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
PM5 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
PM6 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
PP1 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
PP2 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
PP3 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
PP4 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
PP5 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
BA1 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
BS1 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
BS2 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
BS3 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
BS4 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
BP1 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
BP2 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
BP3 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
BP4 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
BP5 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
BP6 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
BP7 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
Identifiers
- Gene
- DDX41
- Transcript
- NM_016222.2
- Coding (HGVS c.)
- NM_016222.2:c.299-3C>T
- Protein (HGVS p.)
- NP_057306.2:p.?
- GRCh38
- chr5:177516196 G>A
- GRCh37
- chr5:176943197 G>A
- ClinVar
- 1338209
Gene diagram
Every interpreted variant in DDX41, mapped onto the exon structure of NM_016222.2. Select a row to find it on the plot.
DDX41NM_016222.2
Fetching transcript structure from UCSC…
Exons
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Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in DDX41
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Select a row to find it on the plot; use the link to open its page.
| Protein | Location | Classification | Link |
|---|
gnomAD v4.1
20 / 1,614,118 alleles
AF 1.24e-05 · 0 homozygotes · FAF 8.03e-06
gnomAD v2.1
3 / 251,444 alleles
AF 1.19e-05 · 0 homozygotes · FAF 2.92e-06
gnomAD-Canada v1.0
0 / 0 alleles
AF 0 · 0 homozygotes
By genetic ancestry
gnomAD v4.1
AF 1.2e-05 · 20 / 1,614,118 alleles · 0 hom · FAF 8e-06
| Middle Eastern1 / 6,062 | 0.00016 |
| Admixed American1 / 60,030 | 1.7e-05 |
| Remaining individuals1 / 62,502 | 1.6e-05 |
| European (Finnish)1 / 63,932 | 1.6e-05 |
| European (non-Finnish)16 / 1,180,046 | 1.4e-05 |
0 alternate alleles recorded in 5 other groups: Amish, East Asian, South Asian, Ashkenazi Jewish, African/African American.
gnomAD v2.1
AF 1.2e-05 · 3 / 251,444 alleles · 0 hom · FAF 2.9e-06
| Admixed American1 / 34,592 | 2.9e-05 |
| European (non-Finnish)2 / 113,734 | 1.8e-05 |
0 alternate alleles recorded in 6 other groups: African/African American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian.
gnomAD-Canada
AF 0 · 0 / 0 alleles · 0 hom
Statements
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 1.23907e-05; MAF= 0.00124%, 20/1614118 alleles, homozygotes = 0) and has highest observed frequency in the Middle Eastern population (AF= 0.000164962; MAF= 0.01650%, 1/6062 alleles, homozygotes = 0); grpmax FAF= 8.03e-06.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 1.19311e-05; MAF= 0.00119%, 3/251444 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 2.89084e-05; MAF= 0.00289%, 1/34592 alleles, homozygotes = 0); grpmax FAF= 2.92e-06.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI and Pangolin
Other predictors
- REVEL
- Not available
- BayesDel
- Not available
How the predictions were used
PP3 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
BP4 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
BP7 No criterion-specific rationale recorded. Details ▾Hide ▴
No further detail was recorded.
Statement
In silico
In progress — evidence not uploaded yet.
8 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.
Recorded publications
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PMID 17576681 ↗Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.Buratti E et al. · 2007No paper-specific finding is recorded.
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PMID 23619275 ↗ACMG position statement on prenatal/preconception expanded carrier screening.No paper-specific finding is recorded.
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PMID 25730230 ↗Expanded carrier screening in reproductive medicine-points to consider: a joint statement of the American College of Medical Genetics and Genomics, American College of Obstetricians and Gynecologists, National Society of Genetic Counselors, Perinatal Quality Foundation, and Society for Maternal-Fetal Medicine.No paper-specific finding is recorded.
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PMID 25741868 ↗Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.No paper-specific finding is recorded.
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PMID 9536098 ↗Statistical features of human exons and their flanking regions.Zhang MQ · 1998No paper-specific finding is recorded.
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PMID 23037933 ↗Including the initial newborn screening bloodspot collection device serial number on birth certificates: basis and recommendations from the Secretary of Health and Human Services' Advisory Committee on Heritable Disorders in Newborns and Children.Therrell BL et al. · 2013No paper-specific finding is recorded.
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PMID 24394680 ↗Parental permission for pilot newborn screening research: guidelines from the NBSTRN.Botkin JR et al. · 2014No paper-specific finding is recorded.
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PMID 31022120 ↗ACOG Committee Opinion No. 778 Summary: Newborn Screening and the Role of the Obstetrician-Gynecologist.No paper-specific finding is recorded.
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
20 / 1,614,118 recorded alleles
Open source ↗
gnomAD v2.1
Captured gnomAD v2.1 source record
Open source ↗
SpliceAI Lookup
Recorded maximum delta 0.000
Open source ↗
ClinVar
3 Uncertain significance
Open source ↗
COSMIC
Captured COSMIC source record
Open source ↗
ClinGen CSpec
Captured ClinGen CSpec source record
Open source ↗
All source links
- ClinGen CSpec ↗cspec.genome.network/cspec/ui/svi/doc/1625925053
- ClinVar ↗www.ncbi.nlm.nih.gov/clinvar/variation/1338209/
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/5-176943197-G-A?dataset=gnomad_r2_1
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr5-177516196-G-A?dataset=gn…
- gnomAD-Canada ↗http://192.168.4.76:8001/variant/5-177516196-G-A
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_016222.2%3Ac.299-…
- OncoKB ↗www.oncokb.org/gene/DDX41/?
- COSMIC ↗cancer.sanger.ac.uk/cosmic/search?q=DDX41+c.299-3C%3ET
Statements for reports
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 1.23907e-05; MAF= 0.00124%, 20/1614118 alleles, homozygotes = 0) and has highest observed frequency in the Middle Eastern population (AF= 0.000164962; MAF= 0.01650%, 1/6062 alleles, homozygotes = 0); grpmax FAF= 8.03e-06.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 1.19311e-05; MAF= 0.00119%, 3/251444 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 2.89084e-05; MAF= 0.00289%, 1/34592 alleles, homozygotes = 0); grpmax FAF= 2.92e-06.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
ClinVar
In progress — evidence not uploaded yet.
In silico
In progress — evidence not uploaded yet.
Functional
In progress — evidence not uploaded yet.
Somatic
In progress — evidence not uploaded yet.
Literature
In progress — evidence not uploaded yet.