chr8-144512918-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP3BP6
The NM_004260.4(RECQL4):c.2684G>A(p.Arg895Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,583,690 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R895S) has been classified as Uncertain significance.
Frequency
Consequence
NM_004260.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECQL4 | NM_004260.4 | c.2684G>A | p.Arg895Lys | missense_variant | 15/21 | ENST00000617875.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.2684G>A | p.Arg895Lys | missense_variant | 15/21 | 1 | NM_004260.4 | P1 | |
RECQL4 | ENST00000621189.4 | c.1613G>A | p.Arg538Lys | missense_variant | 14/20 | 1 | |||
ENST00000580385.1 | n.271+81C>T | intron_variant, non_coding_transcript_variant | 3 | ||||||
RECQL4 | ENST00000534626.6 | c.857G>A | p.Arg286Lys | missense_variant | 6/8 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152260Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000401 AC: 8AN: 199648Hom.: 0 AF XY: 0.0000370 AC XY: 4AN XY: 108066
GnomAD4 exome AF: 0.0000286 AC: 41AN: 1431430Hom.: 0 Cov.: 67 AF XY: 0.0000282 AC XY: 20AN XY: 709422
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152260Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74398
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Mar 28, 2022 | - - |
RECQL4-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 15, 2024 | The RECQL4 c.2684G>A variant is predicted to result in the amino acid substitution p.Arg895Lys. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.014% of alleles in individuals of East Asian descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Baller-Gerold syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 11, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at