rs750118023
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004260.4(RECQL4):āc.2080G>Cā(p.Gly694Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000452 in 1,548,208 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 8/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004260.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RECQL4 | NM_004260.4 | c.2080G>C | p.Gly694Arg | missense_variant | 13/21 | ENST00000617875.6 | NP_004251.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.2080G>C | p.Gly694Arg | missense_variant | 13/21 | 1 | NM_004260.4 | ENSP00000482313 | P1 | |
ENST00000580385.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000201 AC: 3AN: 149554Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000643 AC: 1AN: 155498Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 82454
GnomAD4 exome AF: 0.00000286 AC: 4AN: 1398654Hom.: 0 Cov.: 46 AF XY: 0.00000145 AC XY: 1AN XY: 689916
GnomAD4 genome AF: 0.0000201 AC: 3AN: 149554Hom.: 0 Cov.: 33 AF XY: 0.0000137 AC XY: 1AN XY: 72936
ClinVar
Submissions by phenotype
Baller-Gerold syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 07, 2024 | This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 694 of the RECQL4 protein (p.Gly694Arg). This variant is present in population databases (no rsID available, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with RECQL4-related conditions. ClinVar contains an entry for this variant (Variation ID: 406929). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt RECQL4 protein function with a positive predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at