chr3-52314348-C-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XM_017006129.2(DNAH1):c.-1812C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,094 control chromosomes in the GnomAD database, including 10,996 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.36 ( 10996 hom., cov: 32)
Consequence
DNAH1
XM_017006129.2 5_prime_UTR
XM_017006129.2 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.77
Publications
14 publications found
Genes affected
DNAH1 (HGNC:2940): (dynein axonemal heavy chain 1) This gene encodes an inner dynein arm heavy chain that provides structural support between the radial spokes and the outer doublet of the sperm tail. Naturally occurring mutations in this gene are associated with primary ciliary dyskinesia and multiple morphological anomalies of the flagella that result in asthenozoospermia and male infertility. Mice with a homozygous knockout of the orthologous gene are viable but have reduced sperm motility and are infertile. [provided by RefSeq, Feb 2017]
DNAH1 Gene-Disease associations (from GenCC):
- spermatogenic failure 18Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae)
- ciliary dyskinesia, primary, 37Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, ClinGen
- primary ciliary dyskinesiaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- non-syndromic male infertility due to sperm motility disorderInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAH1 | XM_017006129.2 | c.-1812C>A | 5_prime_UTR_variant | Exon 1 of 80 | XP_016861618.1 | |||
DNAH1 | XM_017006130.2 | c.-1812C>A | 5_prime_UTR_variant | Exon 1 of 79 | XP_016861619.1 | |||
DNAH1 | XM_017006131.2 | c.-1812C>A | 5_prime_UTR_variant | Exon 1 of 79 | XP_016861620.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|
Frequencies
GnomAD3 genomes AF: 0.358 AC: 54349AN: 151976Hom.: 10990 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
54349
AN:
151976
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.357 AC: 54368AN: 152094Hom.: 10996 Cov.: 32 AF XY: 0.369 AC XY: 27409AN XY: 74328 show subpopulations
GnomAD4 genome
AF:
AC:
54368
AN:
152094
Hom.:
Cov.:
32
AF XY:
AC XY:
27409
AN XY:
74328
show subpopulations
African (AFR)
AF:
AC:
7665
AN:
41506
American (AMR)
AF:
AC:
6886
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
AC:
1325
AN:
3470
East Asian (EAS)
AF:
AC:
3023
AN:
5170
South Asian (SAS)
AF:
AC:
2548
AN:
4826
European-Finnish (FIN)
AF:
AC:
5098
AN:
10562
Middle Eastern (MID)
AF:
AC:
104
AN:
294
European-Non Finnish (NFE)
AF:
AC:
26620
AN:
67962
Other (OTH)
AF:
AC:
783
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.494
Heterozygous variant carriers
0
1660
3320
4981
6641
8301
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
530
1060
1590
2120
2650
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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