17-58205727-AC-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_017777.4(MKS1):c.*351delG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.051 in 1,352,134 control chromosomes in the GnomAD database, including 2,171 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.039 ( 190 hom., cov: 31)
Exomes 𝑓: 0.053 ( 1981 hom. )
Consequence
MKS1
NM_017777.4 3_prime_UTR
NM_017777.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.160
Genes affected
MKS1 (HGNC:7121): (MKS transition zone complex subunit 1) The protein encoded by this gene localizes to the basal body and is required for formation of the primary cilium in ciliated epithelial cells. Mutations in this gene result in Meckel syndrome type 1 and in Bardet-Biedl syndrome type 13. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 17-58205727-AC-A is Benign according to our data. Variant chr17-58205727-AC-A is described in ClinVar as [Benign]. Clinvar id is 1277626.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-58205727-AC-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0603 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0389 AC: 5925AN: 152148Hom.: 190 Cov.: 31
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GnomAD3 exomes AF: 0.0365 AC: 5531AN: 151520Hom.: 152 AF XY: 0.0349 AC XY: 2837AN XY: 81366
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GnomAD4 exome AF: 0.0525 AC: 63008AN: 1199868Hom.: 1981 Cov.: 30 AF XY: 0.0506 AC XY: 29805AN XY: 588612
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GnomAD4 genome AF: 0.0389 AC: 5925AN: 152266Hom.: 190 Cov.: 31 AF XY: 0.0379 AC XY: 2820AN XY: 74450
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
May 14, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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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