rs377398995
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004260.4(RECQL4):c.1770C>T(p.Leu590=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,610,792 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. L590L) has been classified as Likely benign.
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.1770C>T | p.Leu590= | synonymous_variant | 11/21 | ENST00000617875.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.1770C>T | p.Leu590= | synonymous_variant | 11/21 | 1 | NM_004260.4 | P1 | |
RECQL4 | ENST00000621189.4 | c.699C>T | p.Leu233= | synonymous_variant | 10/20 | 1 | |||
RECQL4 | ENST00000534626.6 | c.141C>T | p.Leu47= | synonymous_variant | 2/8 | 5 | |||
RECQL4 | ENST00000532846.2 | c.627C>T | p.Leu209= | synonymous_variant | 7/9 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000411 AC: 1AN: 243394Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133160
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1458630Hom.: 0 Cov.: 36 AF XY: 0.00000138 AC XY: 1AN XY: 725538
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74326
ClinVar
Submissions by phenotype
Baller-Gerold syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at