rs1061627
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002907.4(RECQL):c.-349C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 161,314 control chromosomes in the GnomAD database, including 41,339 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.68 ( 38125 hom., cov: 27)
Exomes 𝑓: 0.79 ( 3214 hom. )
Consequence
RECQL
NM_002907.4 5_prime_UTR
NM_002907.4 5_prime_UTR
Scores
2
Splicing: ADA: 0.00007014
2
Clinical Significance
Conservation
PhyloP100: -4.25
Genes affected
RECQL (HGNC:9948): (RecQ like helicase) The protein encoded by this gene is a member of the RecQ DNA helicase family. DNA helicases are enzymes involved in various types of DNA repair, including mismatch repair, nucleotide excision repair and direct repair. The encoded protein is involved in the processing of Holliday junctions, the suppression of sister chromatid exchanges, telomere maintenance, and is required for genotoxic stress resistance. Defects in this gene have been associated with several types of cancer. [provided by RefSeq, Jan 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
?
Variant 12-21501473-G-A is Benign according to our data. Variant chr12-21501473-G-A is described in ClinVar as [Benign]. Clinvar id is 679678.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECQL | NM_002907.4 | c.-349C>T | 5_prime_UTR_variant | 1/15 | ENST00000444129.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL | ENST00000444129.7 | c.-349C>T | 5_prime_UTR_variant | 1/15 | 2 | NM_002907.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.679 AC: 102673AN: 151160Hom.: 38107 Cov.: 27
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GnomAD4 exome AF: 0.787 AC: 7902AN: 10036Hom.: 3214 Cov.: 0 AF XY: 0.794 AC XY: 4320AN XY: 5440
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GnomAD4 genome ? AF: 0.679 AC: 102732AN: 151278Hom.: 38125 Cov.: 27 AF XY: 0.690 AC XY: 50949AN XY: 73886
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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 | GeneDx | Jun 18, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
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