rs370660188
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_004260.4(RECQL4):c.1132-8C>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 0.00000868 in 1,612,674 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely 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.1132-8C>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.1132-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004260.4 | P1 | |||
RECQL4 | ENST00000621189.4 | c.61-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
RECQL4 | ENST00000524998.1 | c.654-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 3 | |||||
RECQL4 | ENST00000532846.2 | c.17-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 34
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1460474Hom.: 0 Cov.: 65 AF XY: 0.00000826 AC XY: 6AN XY: 726508
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74340
ClinVar
Submissions by phenotype
Baller-Gerold syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 23, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at