rs4789223
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004259.7(RECQL5):c.1229+5367C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,082 control chromosomes in the GnomAD database, including 18,871 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.47 ( 18871 hom., cov: 32)
Consequence
RECQL5
NM_004259.7 intron
NM_004259.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.249
Genes affected
RECQL5 (HGNC:9950): (RecQ like helicase 5) The protein encoded by this gene is a helicase that is important for genome stability. The encoded protein also prevents aberrant homologous recombination by displacing RAD51 from ssDNA. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECQL5 | NM_004259.7 | c.1229+5367C>T | intron_variant | ENST00000317905.10 | |||
RECQL5 | XM_005257818.5 | c.1229+5367C>T | intron_variant | ||||
RECQL5 | XM_047437085.1 | c.1229+5367C>T | intron_variant | ||||
RECQL5 | XM_047437091.1 | c.1229+5367C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL5 | ENST00000317905.10 | c.1229+5367C>T | intron_variant | 1 | NM_004259.7 | P1 | |||
RECQL5 | ENST00000423245.6 | c.1148+5367C>T | intron_variant | 1 | |||||
RECQL5 | ENST00000578201.5 | c.1229+5367C>T | intron_variant | 5 | |||||
RECQL5 | ENST00000582464.5 | c.*123+4698C>T | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.468 AC: 71141AN: 151964Hom.: 18864 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.468 AC: 71160AN: 152082Hom.: 18871 Cov.: 32 AF XY: 0.469 AC XY: 34872AN XY: 74340
GnomAD4 genome
?
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71160
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152082
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32
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34872
AN XY:
74340
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1639
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at