rs200732690
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_004260.4(RECQL4):c.1576C>T(p.Leu526Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000404 in 1,611,946 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004260.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.1576C>T | p.Leu526Phe | missense_variant | Exon 9 of 21 | 1 | NM_004260.4 | ENSP00000482313.2 | ||
RECQL4 | ENST00000621189.4 | c.505C>T | p.Leu169Phe | missense_variant | Exon 8 of 20 | 1 | ENSP00000483145.1 | |||
RECQL4 | ENST00000532846.2 | c.430C>T | p.Leu144Phe | missense_variant | Exon 5 of 9 | 5 | ENSP00000476551.1 | |||
RECQL4 | ENST00000688394.1 | n.599C>T | non_coding_transcript_exon_variant | Exon 3 of 4 |
Frequencies
GnomAD3 genomes AF: 0.000414 AC: 63AN: 152200Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000763 AC: 187AN: 245232Hom.: 1 AF XY: 0.000680 AC XY: 91AN XY: 133874
GnomAD4 exome AF: 0.000403 AC: 588AN: 1459628Hom.: 2 Cov.: 33 AF XY: 0.000424 AC XY: 308AN XY: 726020
GnomAD4 genome AF: 0.000414 AC: 63AN: 152318Hom.: 0 Cov.: 34 AF XY: 0.000389 AC XY: 29AN XY: 74486
ClinVar
Submissions by phenotype
Rapadilino syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Nov 08, 2018 | This variant was classified as: Benign. The following ACMG criteria were applied in classifying this variant: BS1,BS2. - |
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Feb 01, 2025 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | RECQL4: BP4 - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Rothmund-Thomson syndrome type 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | curation | Sema4, Sema4 | Jul 22, 2021 | - - |
Baller-Gerold syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 28, 2025 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at