16-84175952-T-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_178452.6(DNAAF1):āc.1718T>Cā(p.Ile573Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000439 in 1,614,190 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. I573I) has been classified as Likely benign.
Frequency
Consequence
NM_178452.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAAF1 | NM_178452.6 | c.1718T>C | p.Ile573Thr | missense_variant | 11/12 | ENST00000378553.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAAF1 | ENST00000378553.10 | c.1718T>C | p.Ile573Thr | missense_variant | 11/12 | 1 | NM_178452.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00221 AC: 336AN: 152212Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000581 AC: 146AN: 251458Hom.: 1 AF XY: 0.000456 AC XY: 62AN XY: 135912
GnomAD4 exome AF: 0.000250 AC: 366AN: 1461860Hom.: 0 Cov.: 35 AF XY: 0.000235 AC XY: 171AN XY: 727220
GnomAD4 genome AF: 0.00225 AC: 342AN: 152330Hom.: 2 Cov.: 33 AF XY: 0.00252 AC XY: 188AN XY: 74496
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Mar 07, 2022 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at