chr17-75628385-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_004259.7(RECQL5):c.2638G>A(p.Val880Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000193 in 1,613,998 control chromosomes in the GnomAD database, including 4 homozygotes. 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 Likely benign (★★).
Frequency
Consequence
NM_004259.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECQL5 | NM_004259.7 | c.2638G>A | p.Val880Ile | missense_variant | 18/20 | ENST00000317905.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL5 | ENST00000317905.10 | c.2638G>A | p.Val880Ile | missense_variant | 18/20 | 1 | NM_004259.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000422 AC: 105AN: 248856Hom.: 2 AF XY: 0.000511 AC XY: 69AN XY: 135132
GnomAD4 exome AF: 0.000202 AC: 295AN: 1461692Hom.: 4 Cov.: 32 AF XY: 0.000282 AC XY: 205AN XY: 727156
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74464
ClinVar
Submissions by phenotype
RECQL5-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 21, 2022 | 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). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | RECQL5: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at