rs942704068
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_004260.4(RECQL4):c.85-4A>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000256 in 1,482,996 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004260.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECQL4 | NM_004260.4 | c.85-4A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000617875.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000621189.4 | c.-991A>T | 5_prime_UTR_variant | 1/20 | 1 | ||||
RECQL4 | ENST00000617875.6 | c.85-4A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004260.4 | P1 | |||
RECQL4 | ENST00000534538.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151710Hom.: 0 Cov.: 34
GnomAD4 exome AF: 0.0000278 AC: 37AN: 1331286Hom.: 0 Cov.: 32 AF XY: 0.0000244 AC XY: 16AN XY: 656498
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151710Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74140
ClinVar
Submissions by phenotype
RECQL4-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 09, 2021 | 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 | Dec 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at