About SOX17
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
SOX17 c.972_977dup, p.(Gln324_His325dup)
Classification
Benign
Variant description:
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is benign. Select a step to read what it means.
Benign.A benign classification under the recorded framework.
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 Not recorded. 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: 3
Pathogenic criteria applied · 0
No pathogenic criterion marked as applied in the recorded assessment.
Benign criteria applied · 3
BA1Stand alone
BA1 · stand alone
This variant is present at an allele frequency of 1.11% in gnomAD v4.1 (17,140/1,543,370 alleles, 139 homozygotes), exceeding the BA1 threshold of >1%. The highest subpopulation frequency is 1.32% in European (non-Finnish) (15,213/1,148,906 alleles, 122 homozygotes). The variant is too common to be a cause of a rare Mendelian disorder.
BS1Strong
BS1 · strong
This variant is present at an allele frequency of 0.722% in gnomAD v2.1 (1,232/170,616 alleles, 10 homozygotes), exceeding the BS1 threshold of >0.3%. The highest subpopulation frequency is 1.21% in European (non-Finnish) (824/68,336 alleles, 7 homozygotes). The variant is more common than expected for a pathogenic variant causing a rare disorder.
BP3Supporting
BP3 · supporting
NM_022454.3:c.972_977dup encodes an in-frame duplication of Gln324 and His325 (p.Gln324_His325dup), which reside within a repetitive low-complexity poly-QH tract in the C-terminal region of SOX17. The native sequence contains multiple QH dipeptide repeats (QMQPQHQHQHQHQHQHH...), and the duplication inserts an additional QH unit into this repetitive region. In-frame duplications within repetitive regions without known function are consistent with benign variation under BP3.
Recorded classification: Benign
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BA1 stand-alone benign, BS1 strong benign, BP3 supporting benign; combination = 1 stand-alone benign + 1 strong benign + 1 supporting benign, which maps to Benign.
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
17,140 / 1,543,370 alleles
gnomAD v4.1: 17,140 / 1,543,370 alleles. Recorded AF 0.0111056. Recorded homozygote count 139.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 0.00722089; MAF= 0.72209%, 1232/170616 alleles, homozygotes = 10) and has highest observed frequency in the European (non-Finnish) population (AF= 0.0120581; MAF= 1.20581%, 824/68336 alleles, homozygotes = 7); grpmax FAF= 0.0118218.
gnomAD-Canada
This variant is present in gnomAD-Canada v1.0 (AF= 0.010005437737901033, 184/18390 alleles, homozygotes = 1).
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
2 Benign · 1 Likely benign. ClinVar API review status: criteria provided, conflicting classifications.
Context only
ClinVar ↗
Functional evidence
Statement recorded
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. SOX17 encodes a transcription factor involved in embryonic development and cell fate. Methylation and downregulation of SOX17 are found in colon, live
No listed criterion applied
OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
3 recorded samples
This variant has previously been reported in somatic cancers (COSMIC; COSV52026813, n = 3 times).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.
Context only
For specialists
Technical detail
ACMG/AMP criteria under Not recorded, with the data and sources behind each one.
29 criteria with recorded statuses: 3 met · 21 not met · 0 not assessed · 5 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
BA1 is met: this variant has an allele frequency of 1.11% in gnomAD v4.1 (17,140/1,543,370 alleles, 139 homozygotes), exceeding the stand-alone benign threshold of >1%.
BS1 is met: the variant is present at 0.722% in gnomAD v2.1 (1,232/170,616 alleles, 10 homozygotes), exceeding the strong benign threshold of >0.3%.
BP3 is met: the variant is an in-frame duplication (p.Gln324_His325dup) within a repetitive low-complexity poly-QH tract in the SOX17 C-terminal region, consistent with a benign in-frame insertion in a repetitive region without known function.
Under generic ACMG/AMP 2015 combination rules, BA1 alone is sufficient for a Benign classification. Independently, BS1 (strong benign) plus BP3 (supporting benign) also exceeds the Likely Benign threshold of one strong benign plus one supporting benign criterion.
The variant is classified in ClinVar as Benign (2 clinical laboratories) and Likely benign (1 clinical laboratory) under Variation ID 915867, consistent with the population evidence.
No criteria match.
Met · 3
BA1 Stand aloneThis variant is present at an allele frequency of 1.11% in gnomAD v4.1 (17,140/1,543,370 alleles, 139 homozygotes), exceeding the BA1 threshold of >1%. The highest subpopulation frequency is 1.32% in European (non-Finnish) (15,213/1,148,906 alleles, 122 homozygotes). The variant is too common to be a cause of a rare Mendelian disorder. Details ▾Hide ▴
Evidence considered
- gnomAD v4.1: AF=1.11% (17
- 140/1
- 543
- 370 alleles)
- 139 homozygotes. NFE subpopulation: AF=1.32%
- 122 homozygotes. Exceeds 1% BA1 threshold. Multiple homozygotes confirm benign population polymorphism.
Sources
BS1 StrongThis variant is present at an allele frequency of 0.722% in gnomAD v2.1 (1,232/170,616 alleles, 10 homozygotes), exceeding the BS1 threshold of >0.3%. The highest subpopulation frequency is 1.21% in European (non-Finnish) (824/68,336 alleles, 7 homozygotes). The variant is more common than expected for a pathogenic variant causing a rare disorder. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1: AF=0.722% (1
- 232/170
- 616 alleles)
- 10 homozygotes. NFE subpopulation: AF=1.21%. Exceeds 0.3% BS1 threshold. Multiple homozygotes observed.
Sources
BP3 SupportingNM_022454.3:c.972_977dup encodes an in-frame duplication of Gln324 and His325 (p.Gln324_His325dup), which reside within a repetitive low-complexity poly-QH tract in the C-terminal region of SOX17. The native sequence contains multiple QH dipeptide repeats (QMQPQHQHQHQHQHQHH...), and the duplication inserts an additional QH unit into this repetitive region. In-frame duplications within repetitive regions without known function are consistent with benign variation under BP3. Details ▾Hide ▴
Evidence considered
- Protein context: p.Gln324_His325dup falls within repetitive poly-QH tract (QHQHQHQHQHQH...). The duplication adds one additional QH repeat unit to an already repetitive low-complexity region. No known critical function assigned to this region.
Sources
Not met · 21 · evaluated, threshold not reached
PVS1 NM_022454.3:c.972_977dup is an in-frame duplication (p.Gln324_His325dup) that does not qualify as a null variant under the ClinGen SVI PVS1 decision tree (PMC6185798). It is not a nonsense, frameshift, or canonical ±1,2 splice site variant. No alternative PVS1 mechanism (e.g., initiation codon disruption, exon deletion) applies. Details ▾Hide ▴
Evidence considered
- In-frame duplication of 6 bp (2 amino acids) in exon 2
- variant bucket classified as 'other' by PVS1 scaffold — not eligible for default PVS1 strength assignments under PMC6185798.
Sources
PS2 No de novo occurrence data available for this variant. No publications report confirmed de novo observation of NM_022454.3:c.972_977dup with maternity and paternity confirmed. Details ▾Hide ▴
Evidence considered
- No de novo reports identified in ClinVar submissions or literature.
Still missing
- No segregation or family studies available for this variant.
PS3 No functional data exists for NM_022454.3:c.972_977dup or a systematically characterized range that includes this position. OncoKB classifies this variant as 'Unknown Oncogenic Effect' with no variant-specific functional evidence. No publications were identified that report experimental functional assays for this variant or for a tiling/saturation mutagenesis study covering residue 324–325. Details ▾Hide ▴
Evidence considered
- OncoKB: Unknown Oncogenic Effect — no variant-specific reviewed functional evidence. No functional publications identified for this exact variant or a characterized range spanning positions 324–325.
Still missing
- No functional characterization of the C-terminal poly-QH region of SOX17 available.
Sources
PS4 This variant is common in the general population (gnomAD v4.1 AF = 1.11%, 139 homozygotes), inconsistent with a pathogenic variant enriched in affected individuals. No case-control studies demonstrating enrichment in disease cohorts were identified. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1: AF=0.722%
- 1232/170616 alleles
- 10 homozygotes. gnomAD v4.1: AF=1.11%
- 17140/1543370 alleles
- 139 homozygotes. High population frequency precludes disease enrichment analysis.
Sources
PM1 Position 324–325 resides in the C-terminal poly-QH repetitive region of SOX17, outside of the HMG-box DNA-binding domain (residues ~67–135). This is not a well-characterized functional domain, and cancerhotspots.org does not identify a statistically significant hotspot at this residue. No literature defines a critical functional domain spanning positions 324–325. Details ▾Hide ▴
Evidence considered
- SOX17 HMG-box domain: residues ~67–135. Variant at 324–325 lies in C-terminal low-complexity QH-repeat region. Cancer Hotspots: residue not significant.
Still missing
- Functional characterization of the SOX17 C-terminal transactivation domain is limited.
Sources
PM2 This variant is common in population databases. gnomAD v4.1 allele frequency is 1.11% (17,140/1,543,370 alleles, 139 homozygotes), far exceeding the PM2 threshold of <0.1%. The variant is also present in gnomAD v2.1 at 0.722% (1,232/170,616 alleles, 10 homozygotes). Details ▾Hide ▴
Evidence considered
- gnomAD v4.1: AF=1.11% >> 0.1% PM2 threshold. gnomAD v2.1: AF=0.722% >> 0.1% PM2 threshold. High allele counts and multiple homozygotes in both databases.
Sources
PM4 Although NM_022454.3:c.972_977dup is an in-frame duplication that alters protein length (p.Gln324_His325dup), it occurs within a repetitive low-complexity poly-QH region and is present at high frequency in the general population (gnomAD v4.1 AF = 1.11%, 139 homozygotes). The high population frequency and location in a repetitive region indicate this is a benign length polymorphism rather than a pathogenic protein length change. Details ▾Hide ▴
Evidence considered
- In-frame duplication in a repetitive poly-QH region. gnomAD v4.1: AF=1.11%
- 139 homozygotes. gnomAD v2.1: AF=0.722%
- 10 homozygotes. High population frequency indicates benign polymorphism.
Sources
PM6 No de novo reports identified for NM_022454.3:c.972_977dup. PM6 requires a confirmed de novo observation with both maternity and paternity confirmed. No publications or ClinVar submissions report de novo occurrence of this variant. Details ▾Hide ▴
Evidence considered
- No de novo observations reported in ClinVar or literature.
Still missing
- No family studies available.
PP1 No segregation data available for this variant. No family studies or co-segregation analyses were identified in ClinVar submissions or the literature. Details ▾Hide ▴
Evidence considered
- No segregation or family data available.
Still missing
- No family studies or co-segregation data available.
PP2 PP2 applies to missense variants in genes with a low rate of benign missense variation and where missense changes are a common disease mechanism. NM_022454.3:c.972_977dup is an in-frame duplication, not a missense variant. Additionally, SOX17 is not established as having a low rate of benign missense variation. Details ▾Hide ▴
Evidence considered
- Variant is an in-frame duplication
- not missense. PP2 not applicable to this variant class.
PP3 In silico pathogenicity predictors (REVEL, BayesDel) are not available for duplication variants. SpliceAI predicts no splice impact (max delta score = 0.00). No HCI prior probability score is available for SOX17. There are no multiple lines of computational evidence supporting a deleterious effect. Details ▾Hide ▴
Evidence considered
- REVEL/BayesDel: not available for non-SNV variants. SpliceAI: max delta = 0.00 (no predicted splice impact). HCI prior: gene not supported.
Still missing
- No in silico tools are validated for assessing pathogenicity of in-frame duplications.
Sources
PP4 No patient phenotype or clinical data were provided for this case. PP4 requires that the variant be identified in an individual with a phenotype and family history highly specific for the gene/disease. No such data are available. Details ▾Hide ▴
Evidence considered
- No patient phenotype data available in case materials.
Still missing
- Clinical phenotype
- family history
- and patient-specific data not provided.
PP5 ClinVar classifies this variant as Benign (2 clinical laboratories) and Likely benign (1 clinical laboratory) with review status 'criteria provided, single submitter' (ClinVar Variation ID: 915867). PP5 requires a 3-star expert panel review for supporting-level application. The single-submitter review status does not meet this threshold. Furthermore, the ClinVar classification is benign, not pathogenic. Details ▾Hide ▴
Evidence considered
- ClinVar Variation ID 915867: Benign (2 labs)
- Likely benign (1 lab). Review status: criteria provided
- single submitter (1-star). Does not meet 3-star expert panel threshold for PP5.
Sources
BS2 BS2 requires observation in a healthy adult individual for a disorder with full penetrance expected at an early age. While multiple homozygotes (n=139) are observed in gnomAD v4.1, this constitutes population-level data rather than individual-level clinical confirmation of healthy adult status with expected disease phenotype absent. The gnomAD data are captured under BA1/BS1. Details ▾Hide ▴
Evidence considered
- gnomAD homozygote counts suggest benign nature but do not constitute individual-level healthy adult clinical data with phenotype confirmed absent.
Still missing
- No individual-level clinical phenotype data available for gnomAD homozygotes.
BS3 BS3 requires well-established in vitro or in vivo functional studies showing no damaging effect. No functional studies exist for NM_022454.3:c.972_977dup. OncoKB reports no variant-specific functional evidence. No publications were identified that experimentally assessed the functional consequence of this duplication. Details ▾Hide ▴
Evidence considered
- OncoKB: Unknown Oncogenic Effect — no variant-specific functional evidence. No functional publications identified.
Still missing
- No functional characterization of the C-terminal poly-QH region of SOX17.
Sources
BS4 BS4 requires lack of segregation in affected family members. No family studies or segregation data are available for this variant. Details ▾Hide ▴
Evidence considered
- No segregation or family data available.
Still missing
- No segregation data available.
BP1 BP1 applies to missense variants in genes where primarily truncating variants cause disease. NM_022454.3:c.972_977dup is an in-frame duplication, not a missense variant. Additionally, SOX17 has not been established as a gene where only truncating variants cause disease. Details ▾Hide ▴
Evidence considered
- Variant is an in-frame duplication
- not missense. BP1 not applicable to this variant class.
BP2 BP2 requires observation in trans with a pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant. No such data are available for this variant. Details ▾Hide ▴
Evidence considered
- No cis/trans phase data available.
Still missing
- No phase data or co-occurrence observations.
BP4 BP4 requires multiple lines of computational evidence suggesting no impact. For duplication variants, REVEL and BayesDel scores are not available. SpliceAI predicts no splice impact (max delta score = 0.00), but a single line of splicing evidence does not constitute 'multiple lines' under BP4. Insufficient computational evidence is available for this variant type to satisfy BP4. Details ▾Hide ▴
Evidence considered
- SpliceAI: max delta = 0.00 (no predicted splice impact). REVEL/BayesDel: not available for non-SNV variants. Single line of evidence insufficient for BP4.
Still missing
- No validated in silico tools for assessing pathogenicity of in-frame duplications.
Sources
BP5 BP5 requires the variant to be found in a case with an alternate molecular basis for disease. No such data are available in the case materials. Details ▾Hide ▴
Evidence considered
- No alternate molecular diagnosis data available.
Still missing
- No patient phenotype or alternate molecular diagnosis data.
BP6 ClinVar classifies this variant as Benign/Likely benign with review status 'criteria provided, single submitter' (ClinVar Variation ID: 915867). BP6 requires a 3-star expert panel review for supporting-benign application. The single-submitter status does not meet this threshold. The ClinVar benign classification is consistent with the population data but does not independently satisfy BP6 criteria. Details ▾Hide ▴
Evidence considered
- ClinVar Variation ID 915867: Benign (2 labs)
- Likely benign (1 lab). Review status: criteria provided
- single submitter (1-star). Does not meet 3-star expert panel threshold for BP6.
Sources
Not applicable · 5· recorded as not applicable Show reasons ▾Hide reasons ▴
PS1 N/APS1 requires a different nucleotide change at the same position producing the same amino acid change. This is a duplication variant, not a single nucleotide substitution. Details ▾Hide ▴
No further detail was recorded.
PM3 N/ASkipped per adjudication instructions — not assessed for this case. Details ▾Hide ▴
No further detail was recorded.
PM5 N/APM5 requires a missense comparator at the same residue with established pathogenicity. This variant is a duplication (p.Gln324_His325dup), not a missense change. The automated PM5 candidate harvest could not identify eligible same-residue missense comparators. Details ▾Hide ▴
Evidence considered
- PM5 candidate harvest returned no eligible comparators. Variant type (duplication) precludes classic PM5 assessment.
Sources
pm5_candidates
BP7 N/ABP7 applies to synonymous (silent) variants with no predicted splice impact and low nucleotide conservation. NM_022454.3:c.972_977dup is an in-frame duplication, not a synonymous variant. Details ▾Hide ▴
No further detail was recorded.
PS5 N/APS5 requires a different nucleotide change at the same position yielding the same amino acid change with established pathogenicity. This is a duplication variant, not a nucleotide substitution. Details ▾Hide ▴
No further detail was recorded.
Identifiers
- Gene
- SOX17
- Transcript
- NM_022454.3
- Coding (HGVS c.)
- NM_022454.3:c.972_977dup
- Protein (HGVS p.)
- NP_071899.1:p.(Gln324_His325dup)
- GRCh38
- chr8:54459698 A>ACACCAG
- GRCh37
- chr8:55372258 A>ACACCAG
- COSMIC
- COSV52026813
Gene diagram
Every interpreted variant in SOX17, mapped onto the exon structure of NM_022454.3. Select a row to find it on the plot.
SOX17NM_022454.3
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 SOX17
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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
17,140 / 1,543,370 alleles
AF 0.0111 · 139 homozygotes · FAF 0.0131
gnomAD v2.1
1,232 / 170,616 alleles
AF 0.00722 · 10 homozygotes · FAF 0.0118
gnomAD-Canada v1.0
Allele count data not recorded
By genetic ancestry
gnomAD v4.1
AF 0.011 · 17140 / 1,543,370 alleles · 139 hom · FAF 0.013
| European (non-Finnish)15213 / 1,148,906 | 0.013122 hom |
| Remaining individuals605 / 60,150 | 0.016 hom |
| European (Finnish)393 / 48,480 | 0.00812 hom |
| South Asian544 / 84,718 | 0.00647 hom |
| Middle Eastern27 / 5,996 | 0.00452 hom |
| Amish3 / 912 | 0.0033 |
| Admixed American149 / 51,432 | 0.0029 |
| African/African American142 / 73,180 | 0.0019 |
| Ashkenazi Jewish43 / 28,636 | 0.0015 |
| East Asian21 / 40,960 | 0.00051 |
gnomAD v2.1
AF 0.0072 · 1232 / 170,616 alleles · 10 hom · FAF 0.012
| European (non-Finnish)824 / 68,336 | 0.0127 hom |
| Remaining individuals61 / 5,274 | 0.0122 hom |
| European (Finnish)93 / 11,566 | 0.008 |
| South Asian131 / 23,210 | 0.00561 hom |
| Admixed American72 / 25,858 | 0.0028 |
| Ashkenazi Jewish18 / 8,450 | 0.0021 |
| African/African American25 / 15,520 | 0.0016 |
| East Asian8 / 12,402 | 0.00065 |
gnomAD-Canada
AF not recorded · ? / ? alleles
Statements
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 0.0111056; MAF= 1.11056%, 17140/1543370 alleles, homozygotes = 139) and has highest observed frequency in the European (non-Finnish) population (AF= 0.0132413; MAF= 1.32413%, 15213/1148906 alleles, homozygotes = 122); grpmax FAF= 0.0130646.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 0.00722089; MAF= 0.72209%, 1232/170616 alleles, homozygotes = 10) and has highest observed frequency in the European (non-Finnish) population (AF= 0.0120581; MAF= 1.20581%, 824/68336 alleles, homozygotes = 7); grpmax FAF= 0.0118218.
gnomAD-Canada
This variant is present in gnomAD-Canada v1.0 (AF= 0.010005437737901033, 184/18390 alleles, homozygotes = 1).
SpliceAI and Pangolin
Other predictors
- REVEL
- Not available
- BayesDel
- Not available
How the predictions were used
PP3 In silico pathogenicity predictors (REVEL, BayesDel) are not available for duplication variants. SpliceAI predicts no splice impact (max delta score = 0.00). No HCI prior probability score is available for SOX17. There are no multiple lines of computational evidence supporting a deleterious effect. Details ▾Hide ▴
Evidence considered
- REVEL/BayesDel: not available for non-SNV variants. SpliceAI: max delta = 0.00 (no predicted splice impact). HCI prior: gene not supported.
Still missing
- No in silico tools are validated for assessing pathogenicity of in-frame duplications.
Sources
BP4 BP4 requires multiple lines of computational evidence suggesting no impact. For duplication variants, REVEL and BayesDel scores are not available. SpliceAI predicts no splice impact (max delta score = 0.00), but a single line of splicing evidence does not constitute 'multiple lines' under BP4. Insufficient computational evidence is available for this variant type to satisfy BP4. Details ▾Hide ▴
Evidence considered
- SpliceAI: max delta = 0.00 (no predicted splice impact). REVEL/BayesDel: not available for non-SNV variants. Single line of evidence insufficient for BP4.
Still missing
- No validated in silico tools for assessing pathogenicity of in-frame duplications.
Sources
BP7 N/ABP7 applies to synonymous (silent) variants with no predicted splice impact and low nucleotide conservation. NM_022454.3:c.972_977dup is an in-frame duplication, not a synonymous variant. Details ▾Hide ▴
No further detail was recorded.
Statement
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
2 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
-
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.Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the ACMG and AMP. This paper defines the ACMG/AMP 2015 variant classification framework and combination rules. It does not mention SOX17 or NM_022454.3:c.972_977dup.Does not name this variant
-
PMID 28492532 ↗Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. This paper provides refined classification rules and thresholds. It does not mention SOX17 or NM_022454.3:c.972_977dup.Does not name this variant
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
17,140 / 1,543,370 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
2 Benign · 1 Likely benign
Open source ↗
COSMIC
Captured COSMIC source record
Open source ↗
Cancer hotspots
Captured Cancer Hotspots source record
Open source ↗
OncoKB
Captured OncoKB source record
Open source ↗
All source links
- ClinVar ↗www.ncbi.nlm.nih.gov/clinvar/?term=NM_022454.3%3Ac.972_977dup
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/8-55372258-A-ACACCAG?dataset=…
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr8-54459698-A-ACACCAG?datas…
- gnomAD-Canada ↗http://192.168.4.76:8001/variant/8-54459698-A-ACACCAG
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_022454.3%3Ac.972_…
- OncoKB ↗www.oncokb.org/gene/SOX17/Q324_H325dup
- COSMIC ↗cancer.sanger.ac.uk/cosmic/mutation/overview?id=124996272
- Cancer hotspots ↗www.cancerhotspots.org/
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= 0.0111056; MAF= 1.11056%, 17140/1543370 alleles, homozygotes = 139) and has highest observed frequency in the European (non-Finnish) population (AF= 0.0132413; MAF= 1.32413%, 15213/1148906 alleles, homozygotes = 122); grpmax FAF= 0.0130646.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 0.00722089; MAF= 0.72209%, 1232/170616 alleles, homozygotes = 10) and has highest observed frequency in the European (non-Finnish) population (AF= 0.0120581; MAF= 1.20581%, 824/68336 alleles, homozygotes = 7); grpmax FAF= 0.0118218.
gnomAD-Canada
This variant is present in gnomAD-Canada v1.0 (AF= 0.010005437737901033, 184/18390 alleles, homozygotes = 1).
ClinVar
This variant has been reported in ClinVar as Benign (2 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 915867)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
Functional
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. SOX17 encodes a transcription factor involved in embryonic development and cell fate. Methylation and downregulation of SOX17 are found in colon, live
Somatic
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV52026813, n = 3 times).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.