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RECQL4
Final classification
Benign
RECQL4 c.2569_2574del · p.Cys857_Thr858del
RECQL4

NM_004260.3:c.2569_2574del (p.Cys857_Thr858del) is an in-frame deletion of 6 nucleotides in exon 15 of RECQL4, encoding a DNA helicase associated with Rothmund-Thomson syndrome (autosomal recessive) and cancer predisposition.

Gene
RECQL4
Transcript
NM_004260.3
HGVS · transcript:coding
NM_004260.3:c.2569_2574del
Consequence
N/A
GRCh38
chr8:144513027 TGGTGCA>T
GRCh37
chr8:145738410 TGGTGCA>T
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: BA1 stand-alone benign, BS1 strong benign, BS2 strong benign, BP6 supporting benign; combination = 1 stand-alone benign + 2 strong benign + 1 supporting benign, which maps to 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, BS2 strong benign, BP6 supporting benign; combination = 1 stand-alone benign + 2 strong benign + 1 supporting benign, which maps to Benign.
Classification rationale
BA1BS1BS2BP6 Benign
RECQL4 c.2569_2574del

NM_004260.3:c.2569_2574del (p.Cys857_Thr858del) is an in-frame deletion of 6 nucleotides in exon 15 of RECQL4, encoding a DNA helicase associated with Rothmund-Thomson syndrome (autosomal recessive) and cancer predisposition. This variant is present at high frequency in the general population: gnomAD v2.1 reports 1462 alleles out of 218,994 (0.67%) with 30 homozygotes, and a grpmax filtering allele frequency of 3.9% in the Admixed American population. gnomAD v4.1 reports 2479 alleles out of 1,574,460 (0.16%) with 41 homozygotes. The presence of 30 or more healthy homozygotes in population databases is incompatible with pathogenicity for a severe autosomal recessive disorder.1 The variant meets BA1 (stand-alone benign): allele frequency exceeds 1% in the general population (grpmax FAF 3.9% in gnomAD v2.1). It also meets BS1 (strong benign): allele frequency exceeds 0.3% (global AF 0.67% in gnomAD v2.1), and BS2 (strong benign): 30 homozygotes are observed in a population database for a recessive disorder expected to be fully penetrant at an early age.2 ClinVar reports this variant as Benign by 8 clinical laboratories and Likely benign by 1 laboratory (variation ID 135140), meeting BP6 (supporting benign).3 No pathogenic criteria are met. PVS1 is not applicable as this is an in-frame deletion, not a null variant. No functional data (PS3), segregation data (PP1), or case-control data (PS4) support pathogenicity. All in silico evidence (SpliceAI delta 0.00; REVEL/BayesDel unavailable for deletion variants) is neutral. PM2 is not met due to the variant's high population frequency.4 Classification: BENIGN. BA1 alone is sufficient for a benign classification per ACMG/AMP 2015 guidelines. The combination of BA1 + BS1 + BS2 + BP6 provides overwhelming evidence of benignity.5

BA1 + BS1 + BS2 + BP6 Benign
Gene diagram · NM_004260.3 · variants mapped to exon structure
RECQL4 NM_004260.3
Fetching transcript structure from UCSC…
Applied criteria · 4 applied · 17 assessed
Applied · 4
Strength Supporting Moderate Strong Very strong
BA1 stand-alone Benign
This variant is present at high frequency in the general population. The grpmax filtering allele frequency in gnomAD v2.1 is 3.9% (Admixed American population), exceeding the BA1 threshold of >1%. Additionally, 30 homozygotes are observed in gnomAD v2.1 and 41 in v4.1, which is incompatible with a pathogenic variant causing Rothmund-Thomson syndrome (autosomal recessive, severe early-onset disorder).
gnomAD v2.1: 1462/218994 alleles (0.67%)30 homozygotesgrpmax FAF 3.9% (AMR)
BS1 strong Benign
This variant is present in gnomAD v2.1 at an allele frequency of 0.67%, exceeding the BS1 threshold of >0.3% for general population frequency. This frequency is inconsistent with a pathogenic variant causing Rothmund-Thomson syndrome.
gnomAD v2.1 AF 0.67% (1462/218994 alleles)exceeding 0.3% BS1 threshold
BS2 strong Benign
Thirty homozygotes are observed in gnomAD v2.1 and 41 homozygotes in gnomAD v4.1. RECQL4 causes Rothmund-Thomson syndrome (autosomal recessive), a severe disorder with full penetrance expected at an early age. The presence of multiple apparently healthy homozygous adults in a population database is strong evidence that this variant is benign.
30 homozygotes in gnomAD v2.141 homozygotes in gnomAD v4.1all from a general population database of individuals not ascertained for disease
BP6 supporting Benign
This variant has been reported in ClinVar as Benign by 8 clinical laboratories and as Likely benign by 1 clinical laboratory (ClinVar variation ID 135140). Although the aggregate review status is 'criteria provided, single submitter' (1-star), the consistent classification across multiple independent clinical laboratories supports a benign interpretation at supporting strength level.
ClinVar: Benign (8 clinical labs)Likely benign (1 clinical lab)variation ID 135140
Assessed · not applied
Pathogenic
PVS1 NM_004260.3:c.2569_2574del is an in-frame deletion of 6 nucleotides removing residues Cys857 and Thr858.
PS2 No de novo data available for this variant.
PS3 No variant-specific functional data identified for NM_004260.3:c.2569_2574del.
PS4 This variant is present at high frequency in the general population (gnomAD v2.1 AF 0.67%, 30 homozygotes), which is inconsistent with pathogenicity.
PM1 This variant is not located in a statistically significant mutational hotspot (cancerhotspots.org).
PM2 This variant is present at high frequency in gnomAD (v2.1 AF 0.67%, v4.1 AF 0.16%), far exceeding the PM2 threshold of <0.1% for a recessive gene.
PM4 Although this is an in-frame deletion causing a protein length change (loss of 2 residues), the variant is present at high frequency in the general population (gnomAD v2.1 AF 0.67%, 30 homozygotes), which is inconsistent with a pathogenic protein-length-altering variant in a recessive disease gene.
PM6 No de novo data available for this variant.
PP1 No segregation data available for this variant.
PP3 No in silico evidence supports a deleterious effect.
PP4 No patient phenotype data available for assessment.
PP5 ClinVar reports this variant as Benign (8 clinical laboratories) and Likely benign (1 clinical laboratory), not pathogenic.
Benign
BS3 No functional studies demonstrating no deleterious effect are available for this variant.
BS4 No segregation data demonstrating lack of cosegregation with disease is available.
BP2 No cis/trans phase data are available for this variant.
BP3 This is an in-frame deletion of two amino acids.
BP4 SpliceAI predicts no splicing impact (max delta score 0.00), but this represents only a single line of computational evidence.
N/A · 7 PS1 · PM3 · PM5 · PP2 · BP1 · BP5 · BP7
Research & evidence
Population frequency · supports benign
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= 0.00157451; MAF= 0.15745%, 2479/1574460 alleles, homozygotes = 41) and has highest observed frequency in the Admixed American population (AF= 0.0300879; MAF= 3.00879%, 1615/53676 alleles, homozygotes = 36); grpmax FAF= 0.0288668.
v2.1
This variant is present in gnomAD v2.1 (AF= 0.00667598; MAF= 0.66760%, 1462/218994 alleles, homozygotes = 30) and has highest observed frequency in the Admixed American population (AF= 0.041093; MAF= 4.10930%, 1158/28180 alleles, homozygotes = 27); grpmax FAF= 0.0390196.
🇨🇦 CA
This variant is present in gnomAD-Canada v1.0 (AF= 0.0017917254859376697, 33/18418 alleles, homozygotes = 0).
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.16% · 2479 / 1,574,460
41 hom · FAF 2.9%
Admixed American
1615 / 53,676
3%
36 hom
East Asian
525 / 42,554
1.2%
4 hom
Remaining individuals
89 / 61,074
0.15%
1 hom
African/African American
71 / 74,132
0.096%
South Asian
62 / 86,320
0.072%
European (non-Finnish)
117 / 1,161,036
0.01%
+ 4 not observed (European (Finnish), Amish, Middle Eastern, Ashkenazi Jewish)
gnomAD v2.1
0.67% · 1462 / 218,994
30 hom · FAF 3.9%
Admixed American
1158 / 28,180
4.1%
27 hom
East Asian
232 / 14,878
1.6%
3 hom
Remaining individuals
20 / 6,048
0.33%
African/African American
24 / 18,884
0.13%
South Asian
20 / 25,098
0.08%
European (non-Finnish)
8 / 95,634
0.0084%
+ 2 not observed (Ashkenazi Jewish, European (Finnish))
gnomAD Canada 🇨🇦
0.18% · 33 / 18,418
0 hom · FAF 2.1%
indel · split
Latino/Admixed American
25 / 838
3%
East Asian
6 / 1,338
0.45%
South Asian
2 / 1,362
0.15%
+ 6 not observed (African/African American, Ashkenazi Jewish, European (Finnish), Middle Eastern, European (non-Finnish), Remaining individuals)
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Benign (8 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 135140)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. RECQL4 encodes a DNA helicase that is involved in DNA replication and repair. Germline mutations of RECQL4 are associated with Rothmund-Thomson, RAPAD
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 previously been reported in somatic cancers (COSMIC; COSV52879881, n = 5 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 3 PMIDs not cited in assessment
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. CLINVAR
24728327 ↗ Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR