chr8-144515002-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004260.4(RECQL4):c.1554C>T(p.Leu518=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000559 in 1,611,192 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. L518L) has been classified as Uncertain significance.
Frequency
Consequence
NM_004260.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECQL4 | NM_004260.4 | c.1554C>T | p.Leu518= | synonymous_variant | 9/21 | ENST00000617875.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.1554C>T | p.Leu518= | synonymous_variant | 9/21 | 1 | NM_004260.4 | P1 | |
RECQL4 | ENST00000621189.4 | c.483C>T | p.Leu161= | synonymous_variant | 8/20 | 1 | |||
RECQL4 | ENST00000532846.2 | c.411C>T | p.Leu137= | synonymous_variant | 5/9 | 5 | |||
RECQL4 | ENST00000688394.1 | n.577C>T | non_coding_transcript_exon_variant | 3/4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000164 AC: 4AN: 243500Hom.: 0 AF XY: 0.0000226 AC XY: 3AN XY: 133016
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1459006Hom.: 0 Cov.: 33 AF XY: 0.00000827 AC XY: 6AN XY: 725654
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74348
ClinVar
Submissions by phenotype
Baller-Gerold syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at