rs368908286
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The ENST00000617875.6(RECQL4):āc.2724T>Cā(p.Leu908=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00017 in 1,597,868 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.00033 ( 1 hom., cov: 34)
Exomes š: 0.00015 ( 0 hom. )
Consequence
RECQL4
ENST00000617875.6 synonymous
ENST00000617875.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.13
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 -11 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 8-144512878-A-G is Benign according to our data. Variant chr8-144512878-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 239745.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144512878-A-G is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=-2.13 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RECQL4 | NM_004260.4 | c.2724T>C | p.Leu908= | synonymous_variant | 15/21 | ENST00000617875.6 | NP_004251.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.2724T>C | p.Leu908= | synonymous_variant | 15/21 | 1 | NM_004260.4 | ENSP00000482313 | P1 | |
RECQL4 | ENST00000621189.4 | c.1653T>C | p.Leu551= | synonymous_variant | 14/20 | 1 | ENSP00000483145 | |||
ENST00000580385.1 | n.271+41A>G | intron_variant, non_coding_transcript_variant | 3 | |||||||
RECQL4 | ENST00000534626.6 | c.897T>C | p.Leu299= | synonymous_variant | 6/8 | 5 | ENSP00000477457 |
Frequencies
GnomAD3 genomes AF: 0.000328 AC: 50AN: 152214Hom.: 1 Cov.: 34
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GnomAD3 exomes AF: 0.000225 AC: 50AN: 222164Hom.: 0 AF XY: 0.000215 AC XY: 26AN XY: 120860
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GnomAD4 exome AF: 0.000154 AC: 222AN: 1445536Hom.: 0 Cov.: 67 AF XY: 0.000138 AC XY: 99AN XY: 717634
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GnomAD4 genome AF: 0.000328 AC: 50AN: 152332Hom.: 1 Cov.: 34 AF XY: 0.000470 AC XY: 35AN XY: 74492
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 30, 2021 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | RECQL4: BP4, BP7 - |
Baller-Gerold syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 24, 2024 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | curation | Sema4, Sema4 | Nov 10, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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