rs149911093
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_031427.4(DNAL1):c.391+9A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00114 in 1,577,616 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0062 ( 11 hom., cov: 32)
Exomes 𝑓: 0.00059 ( 5 hom. )
Consequence
DNAL1
NM_031427.4 intron
NM_031427.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.45
Genes affected
DNAL1 (HGNC:23247): (dynein axonemal light chain 1) This gene encodes an axonemal dynein light chain which functions as a component of the outer dynein arms complex. This complex acts as the molecular motor that provides the force to move cilia in an ATP-dependent manner. The encoded protein is expressed in tissues with motile cilia or flagella and may be involved in the movement of sperm flagella. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Jan 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 14-73687394-A-G is Benign according to our data. Variant chr14-73687394-A-G is described in ClinVar as [Benign]. Clinvar id is 241618.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00625 (951/152250) while in subpopulation AFR AF= 0.0215 (895/41548). AF 95% confidence interval is 0.0204. There are 11 homozygotes in gnomad4. There are 434 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 11 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAL1 | NM_031427.4 | c.391+9A>G | intron_variant | ENST00000553645.7 | |||
DNAL1 | NM_001201366.2 | c.274+9A>G | intron_variant | ||||
DNAL1 | XM_017021679.3 | c.274+9A>G | intron_variant | ||||
DNAL1 | XM_024449715.2 | c.274+9A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAL1 | ENST00000553645.7 | c.391+9A>G | intron_variant | 1 | NM_031427.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00624 AC: 949AN: 152132Hom.: 11 Cov.: 32
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GnomAD3 exomes AF: 0.00166 AC: 374AN: 224912Hom.: 1 AF XY: 0.00141 AC XY: 173AN XY: 122350
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GnomAD4 exome AF: 0.000595 AC: 848AN: 1425366Hom.: 5 Cov.: 30 AF XY: 0.000487 AC XY: 344AN XY: 706636
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GnomAD4 genome ? AF: 0.00625 AC: 951AN: 152250Hom.: 11 Cov.: 32 AF XY: 0.00583 AC XY: 434AN XY: 74442
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia 16 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: -22
Find out detailed SpliceAI scores and Pangolin per-transcript scores at