17-75627526-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_004259.7(RECQL5):c.2876-4G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000731 in 1,613,772 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 (no stars).
Frequency
Consequence
NM_004259.7 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RECQL5 | NM_004259.7 | c.2876-4G>A | splice_region_variant, intron_variant | Intron 19 of 19 | ENST00000317905.10 | NP_004250.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RECQL5 | ENST00000317905.10 | c.2876-4G>A | splice_region_variant, intron_variant | Intron 19 of 19 | 1 | NM_004259.7 | ENSP00000317636.5 | |||
RECQL5 | ENST00000423245.6 | c.2795-4G>A | splice_region_variant, intron_variant | Intron 19 of 19 | 1 | ENSP00000394820.2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000160 AC: 40AN: 249428Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135384
GnomAD4 exome AF: 0.0000739 AC: 108AN: 1461562Hom.: 0 Cov.: 31 AF XY: 0.0000743 AC XY: 54AN XY: 727092
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74354
ClinVar
Submissions by phenotype
RECQL5-related disorder Benign:1
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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at