rs30175
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001369.3(DNAH5):c.12910-11C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 1,612,616 control chromosomes in the GnomAD database, including 137,296 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001369.3 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAH5 | ENST00000265104.5 | c.12910-11C>T | intron_variant | Intron 74 of 78 | 1 | NM_001369.3 | ENSP00000265104.4 | |||
DNAH5 | ENST00000681290.1 | c.12865-11C>T | intron_variant | Intron 74 of 78 | ENSP00000505288.1 | |||||
DNAH5 | ENST00000683611.1 | n.232C>T | non_coding_transcript_exon_variant | Exon 1 of 5 |
Frequencies
GnomAD3 genomes AF: 0.394 AC: 59889AN: 151896Hom.: 11928 Cov.: 32
GnomAD3 exomes AF: 0.411 AC: 102830AN: 250040Hom.: 21338 AF XY: 0.414 AC XY: 55883AN XY: 135122
GnomAD4 exome AF: 0.413 AC: 603156AN: 1460600Hom.: 125353 Cov.: 36 AF XY: 0.414 AC XY: 300768AN XY: 726608
GnomAD4 genome AF: 0.394 AC: 59950AN: 152016Hom.: 11943 Cov.: 32 AF XY: 0.390 AC XY: 28945AN XY: 74294
ClinVar
Submissions by phenotype
not specified Benign:4
- -
12910-11C>T in intron 74 of DNAH5: This variant is not expected to have clinical significance because it has been identified in 42.3% (3635/8600) of European Am erican chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs30175). -
- -
- -
Primary ciliary dyskinesia 3 Benign:3
- -
- -
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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:2
- -
- -
Primary ciliary dyskinesia Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at