rs1401559978
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004260.4(RECQL4):c.2568C>A(p.Thr856=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000703 in 1,422,512 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. T856T) 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.2568C>A | p.Thr856= | synonymous_variant | 15/21 | ENST00000617875.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.2568C>A | p.Thr856= | synonymous_variant | 15/21 | 1 | NM_004260.4 | P1 | |
RECQL4 | ENST00000621189.4 | c.1497C>A | p.Thr499= | synonymous_variant | 14/20 | 1 | |||
ENST00000580385.1 | n.271+197G>T | intron_variant, non_coding_transcript_variant | 3 | ||||||
RECQL4 | ENST00000534626.6 | c.741C>A | p.Thr247= | synonymous_variant | 6/8 | 5 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome AF: 7.03e-7 AC: 1AN: 1422512Hom.: 0 Cov.: 67 AF XY: 0.00 AC XY: 0AN XY: 704218
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
Baller-Gerold syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at