chr8-144516002-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_004260.4(RECQL4):c.1117C>T(p.Leu373Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000059 in 1,609,306 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. L373L) has been classified as Likely benign.
Frequency
Consequence
NM_004260.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECQL4 | NM_004260.4 | c.1117C>T | p.Leu373Phe | missense_variant | 5/21 | ENST00000617875.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.1117C>T | p.Leu373Phe | missense_variant | 5/21 | 1 | NM_004260.4 | P1 | |
RECQL4 | ENST00000621189.4 | c.46C>T | p.Leu16Phe | missense_variant | 4/20 | 1 | |||
RECQL4 | ENST00000532846.2 | c.4C>T | p.Leu2Phe | missense_variant | 1/9 | 5 | |||
RECQL4 | ENST00000524998.1 | c.640C>T | p.Leu214Phe | missense_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000302 AC: 46AN: 152218Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000101 AC: 25AN: 246630Hom.: 0 AF XY: 0.0000818 AC XY: 11AN XY: 134396
GnomAD4 exome AF: 0.0000336 AC: 49AN: 1456970Hom.: 0 Cov.: 66 AF XY: 0.0000304 AC XY: 22AN XY: 723982
GnomAD4 genome AF: 0.000302 AC: 46AN: 152336Hom.: 0 Cov.: 34 AF XY: 0.000242 AC XY: 18AN XY: 74494
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Aug 14, 2023 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Baller-Gerold syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 05, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at