rs200516441
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000617875.6(RECQL4):c.275C>T(p.Ser92Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00155 in 1,612,184 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/12 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. S92P) has been classified as Benign.
Frequency
Consequence
ENST00000617875.6 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RECQL4 | NM_004260.4 | c.275C>T | p.Ser92Phe | missense_variant | 4/21 | ENST00000617875.6 | NP_004251.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.275C>T | p.Ser92Phe | missense_variant | 4/21 | 1 | NM_004260.4 | ENSP00000482313 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00814 AC: 1240AN: 152258Hom.: 14 Cov.: 34
GnomAD3 exomes AF: 0.00191 AC: 468AN: 245212Hom.: 6 AF XY: 0.00145 AC XY: 195AN XY: 134150
GnomAD4 exome AF: 0.000859 AC: 1254AN: 1459808Hom.: 21 Cov.: 31 AF XY: 0.000738 AC XY: 536AN XY: 726198
GnomAD4 genome AF: 0.00814 AC: 1240AN: 152376Hom.: 14 Cov.: 34 AF XY: 0.00791 AC XY: 589AN XY: 74508
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 11, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 19, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1Other:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 09, 2014 | - - |
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at