rs377339114
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_004260.4(RECQL4):c.1879-9C>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,608,280 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 34)
Exomes 𝑓: 0.000025 ( 0 hom. )
Consequence
RECQL4
NM_004260.4 splice_polypyrimidine_tract, intron
NM_004260.4 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.329
Genes affected
RECQL4 (HGNC:9949): (RecQ like helicase 4) The protein encoded by this gene is a DNA helicase that belongs to the RecQ helicase family. DNA helicases unwind double-stranded DNA into single-stranded DNAs and may modulate chromosome segregation. This gene is predominantly expressed in thymus and testis. Mutations in this gene are associated with Rothmund-Thomson, RAPADILINO and Baller-Gerold syndromes. [provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 8-144514116-G-C is Benign according to our data. Variant chr8-144514116-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 572577.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECQL4 | NM_004260.4 | c.1879-9C>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000617875.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.1879-9C>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004260.4 | P1 | |||
RECQL4 | ENST00000621189.4 | c.808-9C>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
RECQL4 | ENST00000532846.2 | c.734-9C>G | splice_polypyrimidine_tract_variant, intron_variant | 5 | |||||
RECQL4 | ENST00000534626.6 | c.248-9C>G | splice_polypyrimidine_tract_variant, intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152134Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.00000859 AC: 2AN: 232924Hom.: 0 AF XY: 0.0000156 AC XY: 2AN XY: 128056
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GnomAD4 exome AF: 0.0000254 AC: 37AN: 1456146Hom.: 0 Cov.: 36 AF XY: 0.0000290 AC XY: 21AN XY: 724150
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GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152134Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74302
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Baller-Gerold syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
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Name
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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