rs4239008
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_023036.6(DNAI2):c.1722+34G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 506,342 control chromosomes in the GnomAD database, including 185,208 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.77 ( 47068 hom., cov: 26)
Exomes 𝑓: 0.87 ( 138140 hom. )
Consequence
DNAI2
NM_023036.6 intron
NM_023036.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.201
Genes affected
DNAI2 (HGNC:18744): (dynein axonemal intermediate chain 2) The protein encoded by this gene belongs to the dynein intermediate chain family, and is part of the dynein complex of respiratory cilia and sperm flagella. Mutations in this gene are associated with primary ciliary dyskinesia type 9. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 17-74312264-G-A is Benign according to our data. Variant chr17-74312264-G-A is described in ClinVar as [Benign]. Clinvar id is 261645.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAI2 | NM_023036.6 | c.1722+34G>A | intron_variant | ENST00000311014.11 | |||
LOC105371891 | XR_934971.3 | n.277-79C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAI2 | ENST00000311014.11 | c.1722+34G>A | intron_variant | 1 | NM_023036.6 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.769 AC: 114346AN: 148656Hom.: 47065 Cov.: 26
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GnomAD3 exomes AF: 0.867 AC: 124824AN: 144000Hom.: 55094 AF XY: 0.869 AC XY: 67548AN XY: 77774
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GnomAD4 exome AF: 0.875 AC: 312813AN: 357586Hom.: 138140 Cov.: 0 AF XY: 0.874 AC XY: 171097AN XY: 195840
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GnomAD4 genome ? AF: 0.769 AC: 114357AN: 148756Hom.: 47068 Cov.: 26 AF XY: 0.771 AC XY: 55803AN XY: 72336
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Primary ciliary dyskinesia 9 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 10, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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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