3-180679690-A-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000650889.1(CCDC39):n.180T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00179 in 561,648 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0047 ( 5 hom., cov: 32)
Exomes 𝑓: 0.00072 ( 2 hom. )
Consequence
CCDC39
ENST00000650889.1 non_coding_transcript_exon
ENST00000650889.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.636
Genes affected
CCDC39 (HGNC:25244): (coiled-coil domain 39 molecular ruler complex subunit) The protein encoded by this gene is involved in the motility of cilia and flagella. The encoded protein is essential for the assembly of dynein regulatory and inner dynein arm complexes, which regulate ciliary beat. Defects in this gene are a cause of primary ciliary dyskinesia type 14 (CILD14). [provided by RefSeq, Jul 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 3-180679690-A-T is Benign according to our data. Variant chr3-180679690-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 3342394.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00468 (712/152212) while in subpopulation AFR AF= 0.0164 (680/41532). AF 95% confidence interval is 0.0154. There are 5 homozygotes in gnomad4. There are 354 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 5 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00467 AC: 711AN: 152094Hom.: 5 Cov.: 32
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GnomAD3 exomes AF: 0.00103 AC: 142AN: 137682Hom.: 0 AF XY: 0.000845 AC XY: 63AN XY: 74590
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GnomAD4 exome AF: 0.000718 AC: 294AN: 409436Hom.: 2 Cov.: 0 AF XY: 0.000552 AC XY: 125AN XY: 226372
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GnomAD4 genome AF: 0.00468 AC: 712AN: 152212Hom.: 5 Cov.: 32 AF XY: 0.00476 AC XY: 354AN XY: 74412
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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
Feb 10, 2022
GeneDx
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
See Variant Classification Assertion Criteria. -
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at