chr5-13841895-G-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_001369.3(DNAH5):c.5281C>G(p.Arg1761Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000657 in 1,093,802 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 Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1761Q) has been classified as Likely benign.
Frequency
Consequence
NM_001369.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH5 | NM_001369.3 | c.5281C>G | p.Arg1761Gly | missense_variant | 33/79 | ENST00000265104.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH5 | ENST00000265104.5 | c.5281C>G | p.Arg1761Gly | missense_variant | 33/79 | 1 | NM_001369.3 | P4 | |
DNAH5 | ENST00000681290.1 | c.5236C>G | p.Arg1746Gly | missense_variant | 33/79 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00343 AC: 373AN: 108868Hom.: 1 Cov.: 25
GnomAD3 exomes AF: 0.000804 AC: 186AN: 231214Hom.: 0 AF XY: 0.000629 AC XY: 79AN XY: 125594
GnomAD4 exome AF: 0.000348 AC: 343AN: 984888Hom.: 1 Cov.: 26 AF XY: 0.000300 AC XY: 151AN XY: 502836
GnomAD4 genome ? AF: 0.00345 AC: 376AN: 108914Hom.: 1 Cov.: 25 AF XY: 0.00329 AC XY: 162AN XY: 49222
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:3
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 01, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 13, 2017 | 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 specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 10, 2021 | In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 27637763) - |
Primary ciliary dyskinesia 3 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 28, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at