rs368140492
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_004260.4(RECQL4):c.2112C>T(p.Ile704=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000325 in 1,567,998 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. I704I) has been classified as Likely benign.
Frequency
Consequence
NM_004260.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECQL4 | NM_004260.4 | c.2112C>T | p.Ile704= | synonymous_variant | 13/21 | ENST00000617875.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.2112C>T | p.Ile704= | synonymous_variant | 13/21 | 1 | NM_004260.4 | P1 | |
ENST00000580385.1 | n.325G>A | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152142Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000571 AC: 10AN: 175130Hom.: 0 AF XY: 0.0000319 AC XY: 3AN XY: 93988
GnomAD4 exome AF: 0.0000212 AC: 30AN: 1415738Hom.: 0 Cov.: 47 AF XY: 0.0000257 AC XY: 18AN XY: 700218
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152260Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74450
ClinVar
Submissions by phenotype
RECQL4-related condition Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 04, 2023 | 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). - |
Baller-Gerold syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 12, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at