chr7-21599902-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001277115.2(DNAH11):c.2783A>T(p.Asp928Val) variant causes a missense change. The variant allele was found at a frequency of 0.00179 in 1,613,486 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D928N) has been classified as Uncertain significance.
Frequency
Consequence
NM_001277115.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH11 | NM_001277115.2 | c.2783A>T | p.Asp928Val | missense_variant | 15/82 | ENST00000409508.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH11 | ENST00000409508.8 | c.2783A>T | p.Asp928Val | missense_variant | 15/82 | 5 | NM_001277115.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00126 AC: 191AN: 152150Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000942 AC: 234AN: 248282Hom.: 1 AF XY: 0.000958 AC XY: 129AN XY: 134710
GnomAD4 exome AF: 0.00184 AC: 2691AN: 1461336Hom.: 5 Cov.: 31 AF XY: 0.00182 AC XY: 1322AN XY: 726924
GnomAD4 genome ? AF: 0.00126 AC: 191AN: 152150Hom.: 1 Cov.: 33 AF XY: 0.00124 AC XY: 92AN XY: 74328
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill | Sep 26, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
DNAH11-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 22, 2022 | The DNAH11 c.2783A>T variant is predicted to result in the amino acid substitution p.Asp928Val. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.16% of alleles in individuals of European (Non-Finnish) descent including 1 homozygous individual in gnomAD (http://gnomad.broadinstitute.org/variant/7-21639520-A-T). Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Mar 12, 2020 | Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at