5-13721028-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_001369.3(DNAH5):c.12251G>A(p.Arg4084Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000172 in 1,614,066 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R4084W) has been classified as Likely benign.
Frequency
Consequence
NM_001369.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH5 | NM_001369.3 | c.12251G>A | p.Arg4084Gln | missense_variant | 71/79 | ENST00000265104.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH5 | ENST00000265104.5 | c.12251G>A | p.Arg4084Gln | missense_variant | 71/79 | 1 | NM_001369.3 | P4 | |
DNAH5 | ENST00000681290.1 | c.12206G>A | p.Arg4069Gln | missense_variant | 71/79 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000123 AC: 31AN: 251180Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135762
GnomAD4 exome AF: 0.000179 AC: 262AN: 1461820Hom.: 0 Cov.: 31 AF XY: 0.000169 AC XY: 123AN XY: 727222
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74442
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia 3 Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Mar 24, 2017 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
Primary ciliary dyskinesia Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Feb 26, 2020 | - - |
Infertility disorder Uncertain:1
Uncertain significance, no assertion criteria provided | provider interpretation | MAGI's Lab - Research, MAGI Group | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at