rs2721191
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004260.4(RECQL4):c.1772C>T(p.Pro591Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00506 in 1,611,110 control chromosomes in the GnomAD database, including 382 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P591H) has been classified as Uncertain significance.
Frequency
Consequence
NM_004260.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECQL4 | NM_004260.4 | c.1772C>T | p.Pro591Leu | missense_variant | 11/21 | ENST00000617875.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.1772C>T | p.Pro591Leu | missense_variant | 11/21 | 1 | NM_004260.4 | P1 | |
RECQL4 | ENST00000621189.4 | c.701C>T | p.Pro234Leu | missense_variant | 10/20 | 1 | |||
RECQL4 | ENST00000534626.6 | c.143C>T | p.Pro48Leu | missense_variant | 2/8 | 5 | |||
RECQL4 | ENST00000532846.2 | c.629C>T | p.Pro210Leu | missense_variant | 7/9 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0274 AC: 4171AN: 152116Hom.: 190 Cov.: 34
GnomAD3 exomes AF: 0.00647 AC: 1577AN: 243902Hom.: 58 AF XY: 0.00491 AC XY: 655AN XY: 133414
GnomAD4 exome AF: 0.00272 AC: 3965AN: 1458876Hom.: 189 Cov.: 36 AF XY: 0.00231 AC XY: 1678AN XY: 725686
GnomAD4 genome AF: 0.0275 AC: 4186AN: 152234Hom.: 193 Cov.: 34 AF XY: 0.0265 AC XY: 1971AN XY: 74420
ClinVar
Submissions by phenotype
not specified Benign:2Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 05, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 16, 2019 | This variant is associated with the following publications: (PMID: 18504617) - |
Rothmund-Thomson syndrome type 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Baller-Gerold syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Benign, criteria provided, single submitter | curation | Sema4, Sema4 | Sep 10, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at