rs199654783
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_004260.4(RECQL4):āc.1847A>Gā(p.Asn616Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000617 in 1,612,112 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N616D) has been classified as Uncertain significance.
Frequency
Consequence
NM_004260.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECQL4 | NM_004260.4 | c.1847A>G | p.Asn616Ser | missense_variant | 11/21 | ENST00000617875.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.1847A>G | p.Asn616Ser | missense_variant | 11/21 | 1 | NM_004260.4 | P1 | |
RECQL4 | ENST00000621189.4 | c.776A>G | p.Asn259Ser | missense_variant | 10/20 | 1 | |||
RECQL4 | ENST00000534626.6 | c.218A>G | p.Asn73Ser | missense_variant | 2/8 | 5 | |||
RECQL4 | ENST00000532846.2 | c.704A>G | p.Asn235Ser | missense_variant | 7/9 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000678 AC: 103AN: 151878Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000533 AC: 131AN: 245662Hom.: 1 AF XY: 0.000441 AC XY: 59AN XY: 133850
GnomAD4 exome AF: 0.000610 AC: 891AN: 1460116Hom.: 2 Cov.: 36 AF XY: 0.000606 AC XY: 440AN XY: 726342
GnomAD4 genome ? AF: 0.000678 AC: 103AN: 151996Hom.: 0 Cov.: 34 AF XY: 0.000673 AC XY: 50AN XY: 74298
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 31, 2021 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 30995915) - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | curation | Sema4, Sema4 | Jan 18, 2022 | - - |
Baller-Gerold syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at