rs1721359
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_178821.3(DAW1):c.113+1735G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 152,092 control chromosomes in the GnomAD database, including 40,037 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 0.72 ( 40037 hom., cov: 31)
Consequence
DAW1
NM_178821.3 intron
NM_178821.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0310
Genes affected
DAW1 (HGNC:26383): (dynein assembly factor with WD repeats 1) Predicted to act upstream of or within several processes, including cerebrospinal fluid circulation; determination of left/right symmetry; and outer dynein arm assembly. Predicted to be located in cilium and extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.04).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DAW1 | NM_178821.3 | c.113+1735G>A | intron_variant | ENST00000309931.3 | |||
DAW1 | NM_001330004.2 | c.68+1735G>A | intron_variant | ||||
DAW1 | XM_047443536.1 | c.68+1735G>A | intron_variant | ||||
DAW1 | NR_138459.2 | n.172+1735G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DAW1 | ENST00000309931.3 | c.113+1735G>A | intron_variant | 1 | NM_178821.3 | P1 | |||
DAW1 | ENST00000440997.1 | c.68+1735G>A | intron_variant | 4 | |||||
DAW1 | ENST00000373666.6 | c.113+1735G>A | intron_variant, NMD_transcript_variant | 2 | |||||
DAW1 | ENST00000454999.5 | c.*54+1735G>A | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.724 AC: 110003AN: 151976Hom.: 40035 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.724 AC: 110048AN: 152092Hom.: 40037 Cov.: 31 AF XY: 0.720 AC XY: 53543AN XY: 74350
GnomAD4 genome
?
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53543
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2132
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3478
ClinVar
Not reported inComputational 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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at