rs746303718
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_004260.4(RECQL4):āc.2538A>Gā(p.Val846=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000742 in 1,576,528 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: š 0.000079 ( 0 hom., cov: 34)
Exomes š: 0.000074 ( 0 hom. )
Consequence
RECQL4
NM_004260.4 synonymous
NM_004260.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.858
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=-0.71).
BP6
?
Variant 8-144513064-T-C is Benign according to our data. Variant chr8-144513064-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 194508.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.
BP7
?
Synonymous conserved (PhyloP=-0.858 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECQL4 | NM_004260.4 | c.2538A>G | p.Val846= | synonymous_variant | 15/21 | ENST00000617875.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.2538A>G | p.Val846= | synonymous_variant | 15/21 | 1 | NM_004260.4 | P1 | |
RECQL4 | ENST00000621189.4 | c.1467A>G | p.Val489= | synonymous_variant | 14/20 | 1 | |||
ENST00000580385.1 | n.271+227T>C | intron_variant, non_coding_transcript_variant | 3 | ||||||
RECQL4 | ENST00000534626.6 | c.711A>G | p.Val237= | synonymous_variant | 6/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152226Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.0000743 AC: 15AN: 201770Hom.: 0 AF XY: 0.0000363 AC XY: 4AN XY: 110094
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GnomAD4 exome AF: 0.0000737 AC: 105AN: 1424302Hom.: 0 Cov.: 67 AF XY: 0.0000752 AC XY: 53AN XY: 704528
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GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152226Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74364
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 09, 2014 | - - |
Baller-Gerold syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 17, 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