chr19-55161086-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_001256715.2(DNAAF3):c.891G>A(p.Thr297=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000169 in 1,542,944 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 (★★). Synonymous variant affecting the same amino acid position (i.e. T297T) has been classified as Likely benign.
Frequency
Consequence
NM_001256715.2 synonymous
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.891G>A | p.Thr297= | synonymous_variant | 8/12 | ENST00000524407.7 | |
DNAAF3-AS1 | XR_007067344.1 | n.178C>T | non_coding_transcript_exon_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAAF3 | ENST00000524407.7 | c.891G>A | p.Thr297= | synonymous_variant | 8/12 | 1 | NM_001256715.2 | A2 | |
DNAAF3-AS1 | ENST00000591665.1 | n.1008C>T | non_coding_transcript_exon_variant | 3/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000345 AC: 5AN: 144736Hom.: 0 AF XY: 0.0000384 AC XY: 3AN XY: 78082
GnomAD4 exome AF: 0.00000647 AC: 9AN: 1390712Hom.: 0 Cov.: 34 AF XY: 0.00000874 AC XY: 6AN XY: 686176
GnomAD4 genome AF: 0.000112 AC: 17AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74426
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 29, 2023 | This alteration is classified as likely 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at