rs369306389
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_004260.4(RECQL4):c.1491C>T(p.Ser497=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000243 in 1,606,582 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. S497S) 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 -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECQL4 | NM_004260.4 | c.1491C>T | p.Ser497= | synonymous_variant | 9/21 | ENST00000617875.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.1491C>T | p.Ser497= | synonymous_variant | 9/21 | 1 | NM_004260.4 | P1 | |
RECQL4 | ENST00000621189.4 | c.420C>T | p.Ser140= | synonymous_variant | 8/20 | 1 | |||
RECQL4 | ENST00000532846.2 | c.369-23C>T | intron_variant | 5 | |||||
RECQL4 | ENST00000688394.1 | n.514C>T | non_coding_transcript_exon_variant | 3/4 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152198Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000428 AC: 10AN: 233794Hom.: 0 AF XY: 0.0000235 AC XY: 3AN XY: 127722
GnomAD4 exome AF: 0.0000124 AC: 18AN: 1454384Hom.: 0 Cov.: 33 AF XY: 0.00000830 AC XY: 6AN XY: 723006
GnomAD4 genome AF: 0.000138 AC: 21AN: 152198Hom.: 0 Cov.: 34 AF XY: 0.000121 AC XY: 9AN XY: 74350
ClinVar
Submissions by phenotype
RECQL4-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 23, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Baller-Gerold syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at