chr14-73654843-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_031427.4(DNAL1):c.4-4A>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 0.00132 in 1,188,308 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.4-4A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000553645.7 | |||
DNAL1 | NM_001201366.2 | c.-114-4A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
DNAL1 | XM_017021679.3 | c.-114-4A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
DNAL1 | XM_024449715.2 | c.-114-4A>T | 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.4-4A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_031427.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 3AN: 148814Hom.: 0 Cov.: 31 FAILED QC
GnomAD3 exomes AF: 0.00367 AC: 338AN: 92032Hom.: 0 AF XY: 0.00362 AC XY: 180AN XY: 49670
GnomAD4 exome AF: 0.00132 AC: 1574AN: 1188308Hom.: 0 Cov.: 33 AF XY: 0.00139 AC XY: 811AN XY: 582942
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000201 AC: 3AN: 148908Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 1AN XY: 72566
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia 16 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 06, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at