12-25108825-T-TAAAAAAAA
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_018272.5(DNAI7):c.1894-10_1894-3dupTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0033 ( 19 hom., cov: 0)
Exomes 𝑓: 0.014 ( 18 hom. )
Failed GnomAD Quality Control
Consequence
DNAI7
NM_018272.5 splice_region, intron
NM_018272.5 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.474
Genes affected
DNAI7 (HGNC:29599): (dynein axonemal intermediate chain 7) Predicted to enable beta-tubulin binding activity and microtubule binding activity. Predicted to be located in cilium; cytoplasm; and microtubule cytoskeleton. Predicted to be part of axonemal dynein complex. Predicted to be active in axoneme. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 12-25108825-T-TAAAAAAAA is Benign according to our data. Variant chr12-25108825-T-TAAAAAAAA is described in ClinVar as [Likely_benign]. Clinvar id is 2642790.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0706 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAI7 | NM_018272.5 | c.1894-10_1894-3dupTTTTTTTT | splice_region_variant, intron_variant | ENST00000395987.8 | NP_060742.4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00333 AC: 161AN: 48410Hom.: 19 Cov.: 0
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0138 AC: 782AN: 56656Hom.: 18 Cov.: 13 AF XY: 0.0128 AC XY: 365AN XY: 28422
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GnomAD4 genome AF: 0.00326 AC: 158AN: 48428Hom.: 19 Cov.: 0 AF XY: 0.00377 AC XY: 79AN XY: 20966
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | DNAI7: BS2 - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at