rs368782236
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_004260.4(RECQL4):c.355-8C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00053 in 1,517,598 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_004260.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECQL4 | NM_004260.4 | c.355-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000617875.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.355-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004260.4 | P1 | |||
RECQL4 | ENST00000621189.4 | c.-717-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
RECQL4 | ENST00000524998.1 | c.227+278C>T | intron_variant | 3 | |||||
RECQL4 | ENST00000534538.1 | c.*262-111C>T | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000388 AC: 59AN: 152230Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000513 AC: 87AN: 169498Hom.: 0 AF XY: 0.000708 AC XY: 64AN XY: 90424
GnomAD4 exome AF: 0.000546 AC: 746AN: 1365368Hom.: 0 Cov.: 35 AF XY: 0.000593 AC XY: 397AN XY: 669420
GnomAD4 genome ? AF: 0.000388 AC: 59AN: 152230Hom.: 0 Cov.: 34 AF XY: 0.000430 AC XY: 32AN XY: 74372
ClinVar
Submissions by phenotype
Baller-Gerold syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at