NM_004260.4:c.2756-6C>T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_004260.4(RECQL4):c.2756-6C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000329 in 1,611,422 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004260.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152246Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000245 AC: 6AN: 245166Hom.: 0 AF XY: 0.0000299 AC XY: 4AN XY: 133796
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1459176Hom.: 0 Cov.: 66 AF XY: 0.0000386 AC XY: 28AN XY: 725850
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152246Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74368
ClinVar
Submissions by phenotype
not provided Uncertain:1
RECQL4: PM2, BP4 -
Hereditary cancer-predisposing syndrome Uncertain:1
- -
Baller-Gerold syndrome Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at