rs1411379067
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_015512.5(DNAH1):c.10627-10C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,386 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
DNAH1
NM_015512.5 splice_polypyrimidine_tract, intron
NM_015512.5 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.0001297
2
Clinical Significance
Conservation
PhyloP100: 0.00400
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 -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
?
Variant 3-52394455-C-T is Benign according to our data. Variant chr3-52394455-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 544660.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH1 | NM_015512.5 | c.10627-10C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000420323.7 | |||
DNAH1 | XM_017006129.2 | c.10696-10C>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
DNAH1 | XM_017006130.2 | c.10627-10C>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
DNAH1 | XM_017006131.2 | c.10570-10C>T | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH1 | ENST00000420323.7 | c.10627-10C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_015512.5 | P1 | |||
DNAH1 | ENST00000490713.5 | c.1327-10C>T | splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 5 | |||||
DNAH1 | ENST00000486752.5 | n.11084-10C>T | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 | |||||
DNAH1 | ENST00000488988.5 | n.2413-10C>T | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
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Cov.:
32
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 247194Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134320
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GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461386Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 726970
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GnomAD4 genome ? Cov.: 32
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Spermatogenic failure 18;C4539798:Ciliary dyskinesia, primary, 37 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 17, 2023 | - - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at