8-144515235-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_004260.4(RECQL4):c.1398G>A(p.Pro466=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000846 in 1,588,058 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P466P) has been classified as Likely benign.
Frequency
Consequence
NM_004260.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECQL4 | NM_004260.4 | c.1398G>A | p.Pro466= | synonymous_variant | 8/21 | ENST00000617875.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.1398G>A | p.Pro466= | synonymous_variant | 8/21 | 1 | NM_004260.4 | P1 | |
RECQL4 | ENST00000621189.4 | c.327G>A | p.Pro109= | synonymous_variant | 7/20 | 1 | |||
RECQL4 | ENST00000532846.2 | c.285G>A | p.Pro95= | synonymous_variant | 4/9 | 5 | |||
RECQL4 | ENST00000688394.1 | n.421G>A | non_coding_transcript_exon_variant | 2/4 |
Frequencies
GnomAD3 genomes ? AF: 0.00117 AC: 178AN: 152214Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.00120 AC: 251AN: 208844Hom.: 1 AF XY: 0.00134 AC XY: 152AN XY: 113278
GnomAD4 exome AF: 0.000812 AC: 1166AN: 1435726Hom.: 5 Cov.: 33 AF XY: 0.000881 AC XY: 627AN XY: 712078
GnomAD4 genome ? AF: 0.00116 AC: 177AN: 152332Hom.: 1 Cov.: 34 AF XY: 0.00136 AC XY: 101AN XY: 74492
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 06, 2021 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | RECQL4: BP4, BP7 - |
Baller-Gerold syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 12, 2024 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | curation | Sema4, Sema4 | Oct 07, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at