8-144515143-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_004260.4(RECQL4):c.1483+7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00012 in 1,566,854 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, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RECQL4 | ENST00000617875.6 | c.1483+7G>A | splice_region_variant, intron_variant | Intron 8 of 20 | 1 | NM_004260.4 | ENSP00000482313.2 | |||
RECQL4 | ENST00000621189.4 | c.412+7G>A | splice_region_variant, intron_variant | Intron 7 of 19 | 1 | ENSP00000483145.1 | ||||
RECQL4 | ENST00000532846.2 | c.367+7G>A | splice_region_variant, intron_variant | Intron 4 of 8 | 5 | ENSP00000476551.1 | ||||
RECQL4 | ENST00000688394.1 | n.506+7G>A | splice_region_variant, intron_variant | Intron 2 of 3 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152226Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000219 AC: 38AN: 173566Hom.: 0 AF XY: 0.000268 AC XY: 25AN XY: 93178
GnomAD4 exome AF: 0.000124 AC: 175AN: 1414510Hom.: 0 Cov.: 33 AF XY: 0.000153 AC XY: 107AN XY: 699328
GnomAD4 genome AF: 0.0000853 AC: 13AN: 152344Hom.: 0 Cov.: 34 AF XY: 0.000107 AC XY: 8AN XY: 74488
ClinVar
Submissions by phenotype
Rapadilino syndrome Benign:1
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Baller-Gerold syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at