17-75627617-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004259.7(RECQL5):c.2875+6C>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000772 in 1,613,272 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00074 ( 2 hom., cov: 33)
Exomes 𝑓: 0.00078 ( 12 hom. )
Consequence
RECQL5
NM_004259.7 splice_donor_region, intron
NM_004259.7 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.00001522
2
Clinical Significance
Conservation
PhyloP100: 0.815
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 17-75627617-G-A is Benign according to our data. Variant chr17-75627617-G-A is described in ClinVar as [Benign]. Clinvar id is 721351.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECQL5 | NM_004259.7 | c.2875+6C>T | splice_donor_region_variant, intron_variant | ENST00000317905.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL5 | ENST00000317905.10 | c.2875+6C>T | splice_donor_region_variant, intron_variant | 1 | NM_004259.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000736 AC: 112AN: 152228Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.00150 AC: 370AN: 245880Hom.: 3 AF XY: 0.00134 AC XY: 179AN XY: 133842
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GnomAD4 exome AF: 0.000776 AC: 1134AN: 1461044Hom.: 12 Cov.: 31 AF XY: 0.000795 AC XY: 578AN XY: 726824
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GnomAD4 genome AF: 0.000736 AC: 112AN: 152228Hom.: 2 Cov.: 33 AF XY: 0.000834 AC XY: 62AN XY: 74368
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at