rs4244610
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004260.4(RECQL4):c.3236+13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 1,599,570 control chromosomes in the GnomAD database, including 177,531 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.42 ( 14483 hom., cov: 35)
Exomes 𝑓: 0.47 ( 163048 hom. )
Consequence
RECQL4
NM_004260.4 intron
NM_004260.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.90
Genes affected
RECQL4 (HGNC:9949): (RecQ like helicase 4) The protein encoded by this gene is a DNA helicase that belongs to the RecQ helicase family. DNA helicases unwind double-stranded DNA into single-stranded DNAs and may modulate chromosome segregation. This gene is predominantly expressed in thymus and testis. Mutations in this gene are associated with Rothmund-Thomson, RAPADILINO and Baller-Gerold syndromes. [provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 8-144512131-G-A is Benign according to our data. Variant chr8-144512131-G-A is described in ClinVar as [Benign]. Clinvar id is 94893.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512131-G-A is described in Lovd as [Benign]. Variant chr8-144512131-G-A is described in Lovd as [Likely_benign].
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECQL4 | NM_004260.4 | c.3236+13C>T | intron_variant | ENST00000617875.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.3236+13C>T | intron_variant | 1 | NM_004260.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.421 AC: 63981AN: 152070Hom.: 14478 Cov.: 35
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GnomAD3 exomes AF: 0.490 AC: 112458AN: 229620Hom.: 28014 AF XY: 0.493 AC XY: 62073AN XY: 125874
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GnomAD4 exome AF: 0.472 AC: 682849AN: 1447382Hom.: 163048 Cov.: 56 AF XY: 0.476 AC XY: 341743AN XY: 718472
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GnomAD4 genome ? AF: 0.421 AC: 64001AN: 152188Hom.: 14483 Cov.: 35 AF XY: 0.427 AC XY: 31765AN XY: 74404
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ClinVar
Significance: Benign
Submissions summary: Benign:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 08, 2014 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Baller-Gerold syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Rapadilino syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
not provided Benign:1
Likely benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Rothmund-Thomson syndrome type 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at