chr14-73654842-T-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_031427.4(DNAL1):c.4-5T>A 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 0.0000254 in 1,337,600 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 Likely benign (★).
Frequency
Consequence
NM_031427.4 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 |
---|---|---|---|---|---|---|---|
DNAL1 | NM_031427.4 | c.4-5T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000553645.7 | |||
DNAL1 | NM_001201366.2 | c.-114-5T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
DNAL1 | XM_017021679.3 | c.-114-5T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
DNAL1 | XM_024449715.2 | c.-114-5T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAL1 | ENST00000553645.7 | c.4-5T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_031427.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 150982Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.000115 AC: 13AN: 113184Hom.: 0 AF XY: 0.0000660 AC XY: 4AN XY: 60576
GnomAD4 exome AF: 0.0000254 AC: 34AN: 1337600Hom.: 0 Cov.: 33 AF XY: 0.0000212 AC XY: 14AN XY: 658994
GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 150982Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73694
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 20, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at