17-75628388-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004259.7(RECQL5):c.2635G>A(p.Val879Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000126 in 1,613,850 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. V879V) has been classified as Benign.
Frequency
Consequence
NM_004259.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECQL5 | NM_004259.7 | c.2635G>A | p.Val879Ile | missense_variant | 18/20 | ENST00000317905.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL5 | ENST00000317905.10 | c.2635G>A | p.Val879Ile | missense_variant | 18/20 | 1 | NM_004259.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000804 AC: 20AN: 248802Hom.: 0 AF XY: 0.0000666 AC XY: 9AN XY: 135112
GnomAD4 exome AF: 0.000131 AC: 192AN: 1461678Hom.: 0 Cov.: 32 AF XY: 0.000131 AC XY: 95AN XY: 727150
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74332
ClinVar
Submissions by phenotype
RECQL5-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 12, 2024 | The RECQL5 c.2635G>A variant is predicted to result in the amino acid substitution p.Val879Ile. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.013% of alleles in individuals of European (Non-Finnish) descent in gnomAD, but is not listed in ClinVar. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at