rs114272520
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015512.5(DNAH1):c.11249A>G(p.Asn3750Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000719 in 1,613,266 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00030 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000049 ( 0 hom. )
Consequence
DNAH1
NM_015512.5 missense
NM_015512.5 missense
Scores
4
13
Clinical Significance
Conservation
PhyloP100: 5.00
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.017922938).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH1 | NM_015512.5 | c.11249A>G | p.Asn3750Ser | missense_variant | 70/78 | ENST00000420323.7 | |
DNAH1 | XM_017006129.2 | c.11318A>G | p.Asn3773Ser | missense_variant | 72/80 | ||
DNAH1 | XM_017006130.2 | c.11249A>G | p.Asn3750Ser | missense_variant | 71/79 | ||
DNAH1 | XM_017006131.2 | c.11192A>G | p.Asn3731Ser | missense_variant | 71/79 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH1 | ENST00000420323.7 | c.11249A>G | p.Asn3750Ser | missense_variant | 70/78 | 1 | NM_015512.5 | P1 | |
DNAH1 | ENST00000486752.5 | n.11706A>G | non_coding_transcript_exon_variant | 69/77 | 2 | ||||
DNAH1 | ENST00000488988.5 | n.3035A>G | non_coding_transcript_exon_variant | 17/25 | 2 | ||||
DNAH1 | ENST00000490713.5 | c.1949A>G | p.Asn650Ser | missense_variant, NMD_transcript_variant | 13/20 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000296 AC: 45AN: 152130Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000608 AC: 15AN: 246872Hom.: 0 AF XY: 0.0000745 AC XY: 10AN XY: 134290
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GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461018Hom.: 0 Cov.: 32 AF XY: 0.0000509 AC XY: 37AN XY: 726760
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GnomAD4 genome ? AF: 0.000296 AC: 45AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74438
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Spermatogenic failure 18;C4539798:Ciliary dyskinesia, primary, 37 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jul 19, 2022 | This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 3750 of the DNAH1 protein (p.Asn3750Ser). This variant is present in population databases (rs114272520, gnomAD 0.09%). This variant has not been reported in the literature in individuals affected with DNAH1-related conditions. ClinVar contains an entry for this variant (Variation ID: 544608). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Vest4
MVP
MPC
ClinPred
T
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at