17-75630842-G-GTGT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_004259.7(RECQL5):c.1586-6_1586-5insACA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0631 in 1,139,402 control chromosomes in the GnomAD database, including 1,959 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_004259.7 splice_region, 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RECQL5 | NM_004259.7 | c.1586-6_1586-5insACA | splice_region_variant, intron_variant | Intron 11 of 19 | ENST00000317905.10 | NP_004250.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RECQL5 | ENST00000317905.10 | c.1586-6_1586-5insACA | splice_region_variant, intron_variant | Intron 11 of 19 | 1 | NM_004259.7 | ENSP00000317636.5 | |||
RECQL5 | ENST00000423245.6 | c.1505-6_1505-5insACA | splice_region_variant, intron_variant | Intron 11 of 19 | 1 | ENSP00000394820.2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 6424AN: 108212Hom.: 269 Cov.: 21 FAILED QC
GnomAD3 exomes AF: 0.124 AC: 7134AN: 57474Hom.: 1182 AF XY: 0.122 AC XY: 3536AN XY: 28946
GnomAD4 exome AF: 0.0631 AC: 71928AN: 1139402Hom.: 1959 Cov.: 25 AF XY: 0.0628 AC XY: 35040AN XY: 557830
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0593 AC: 6423AN: 108248Hom.: 269 Cov.: 21 AF XY: 0.0560 AC XY: 2916AN XY: 52056
ClinVar
Submissions by phenotype
not specified Benign:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
RECQL5-related disorder Benign:1
This variant is classified as 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