19-55159098-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001256715.2(DNAAF3):c.1590G>T(p.Pro530Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,456,206 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001256715.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAAF3 | NM_001256715.2 | c.1590G>T | p.Pro530Pro | synonymous_variant | Exon 12 of 12 | ENST00000524407.7 | NP_001243644.1 | |
DNAAF3 | NM_001256714.1 | c.1791G>T | p.Pro597Pro | synonymous_variant | Exon 12 of 12 | NP_001243643.1 | ||
DNAAF3 | NM_178837.4 | c.1731G>T | p.Pro577Pro | synonymous_variant | Exon 12 of 12 | NP_849159.2 | ||
DNAAF3 | NM_001256716.2 | c.1428G>T | p.Pro476Pro | synonymous_variant | Exon 12 of 12 | NP_001243645.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAAF3 | ENST00000524407.7 | c.1590G>T | p.Pro530Pro | synonymous_variant | Exon 12 of 12 | 1 | NM_001256715.2 | ENSP00000432046.3 | ||
ENSG00000267110 | ENST00000587871.1 | n.478+95G>T | intron_variant | Intron 4 of 8 | 5 | ENSP00000473050.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1456206Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 723756
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.