chr19-55162293-AC-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_001256715.2(DNAAF3):c.323-4del 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 0.000999 in 1,249,968 control chromosomes in the GnomAD database, including 11 homozygotes. 1/1 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_001256715.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAAF3 | NM_001256715.2 | c.323-4del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000524407.7 | |||
DNAAF3-AS1 | XR_007067344.1 | n.307-458del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAAF3 | ENST00000524407.7 | c.323-4del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001256715.2 | A2 | |||
DNAAF3-AS1 | ENST00000591665.1 | n.1137-458del | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00497 AC: 757AN: 152208Hom.: 9 Cov.: 33
GnomAD3 exomes AF: 0.00152 AC: 34AN: 22308Hom.: 1 AF XY: 0.00138 AC XY: 14AN XY: 10154
GnomAD4 exome AF: 0.000448 AC: 492AN: 1097642Hom.: 2 Cov.: 31 AF XY: 0.000453 AC XY: 235AN XY: 518306
GnomAD4 genome AF: 0.00497 AC: 757AN: 152326Hom.: 9 Cov.: 33 AF XY: 0.00465 AC XY: 346AN XY: 74488
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 20, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 11, 2016 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 06, 2015 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at