chr1-224964478-G-A
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_001367479.1(DNAH14):c.368-1G>A variant causes a splice acceptor, intron change. The variant allele was found at a frequency of 0.00012 in 1,606,678 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001367479.1 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAH14 | NM_001367479.1 | c.368-1G>A | splice_acceptor_variant, intron_variant | Intron 4 of 85 | ENST00000682510.1 | NP_001354408.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAH14 | ENST00000682510.1 | c.368-1G>A | splice_acceptor_variant, intron_variant | Intron 4 of 85 | NM_001367479.1 | ENSP00000508305.1 |
Frequencies
GnomAD3 genomes AF: 0.0000856 AC: 13AN: 151866Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000109 AC: 27AN: 247620Hom.: 0 AF XY: 0.0000819 AC XY: 11AN XY: 134340
GnomAD4 exome AF: 0.000123 AC: 179AN: 1454812Hom.: 0 Cov.: 30 AF XY: 0.000116 AC XY: 84AN XY: 723508
GnomAD4 genome AF: 0.0000856 AC: 13AN: 151866Hom.: 0 Cov.: 32 AF XY: 0.0000674 AC XY: 5AN XY: 74142
ClinVar
Submissions by phenotype
not provided Uncertain:1
Canonical splice site variant in a gene or region of a gene for which loss of function is not a well-established mechanism of disease; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at