rs34271972
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_004260.4(RECQL4):c.2223C>T(p.Ala741=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000364 in 1,609,842 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A741A) has been classified as Likely benign.
Frequency
Consequence
NM_004260.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECQL4 | NM_004260.4 | c.2223C>T | p.Ala741= | synonymous_variant | 14/21 | ENST00000617875.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.2223C>T | p.Ala741= | synonymous_variant | 14/21 | 1 | NM_004260.4 | P1 | |
RECQL4 | ENST00000621189.4 | c.1152C>T | p.Ala384= | synonymous_variant | 13/20 | 1 | |||
ENST00000580385.1 | n.272-148G>A | intron_variant, non_coding_transcript_variant | 3 | ||||||
RECQL4 | ENST00000534626.6 | c.594C>T | p.Ala198= | synonymous_variant | 5/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00185 AC: 281AN: 152230Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000457 AC: 111AN: 243068Hom.: 0 AF XY: 0.000353 AC XY: 47AN XY: 133222
GnomAD4 exome AF: 0.000209 AC: 304AN: 1457494Hom.: 0 Cov.: 48 AF XY: 0.000194 AC XY: 141AN XY: 725222
GnomAD4 genome ? AF: 0.00185 AC: 282AN: 152348Hom.: 1 Cov.: 33 AF XY: 0.00187 AC XY: 139AN XY: 74502
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 01, 2017 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 09, 2021 | - - |
Baller-Gerold syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | curation | Sema4, Sema4 | Jan 31, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at