20-43637268-CTT-CTTT
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_016004.5(IFT52):c.1120+26dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0396 in 1,128,950 control chromosomes in the GnomAD database, including 11 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0021 ( 3 hom., cov: 33)
Exomes 𝑓: 0.045 ( 8 hom. )
Consequence
IFT52
NM_016004.5 intron
NM_016004.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0880
Genes affected
IFT52 (HGNC:15901): (intraflagellar transport 52) This gene encodes a conserved proline-rich protein that is a component of the intraflagellar transport-B (IFT-B) core complex. The encoded protein is essential for the integrity of the IFT-B core complex, and for biosynthesis and maintenance of cilia. Mutations in this gene are associated with ciliopathy that affects the skeleton. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 20-43637268-C-CT is Benign according to our data. Variant chr20-43637268-C-CT is described in ClinVar as [Benign]. Clinvar id is 1614780.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.0452 (44375/981104) while in subpopulation EAS AF= 0.051 (1388/27220). AF 95% confidence interval is 0.0488. There are 8 homozygotes in gnomad4_exome. There are 22063 alleles in male gnomad4_exome subpopulation. Median coverage is 15. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IFT52 | ENST00000373030.8 | c.1120+15_1120+16insT | intron_variant | 1 | NM_016004.5 | ENSP00000362121.3 | ||||
IFT52 | ENST00000373039.4 | c.1120+15_1120+16insT | intron_variant | 5 | ENSP00000362130.4 | |||||
IFT52 | ENST00000461012.1 | n.107+15_107+16insT | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00209 AC: 309AN: 147778Hom.: 3 Cov.: 33
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GnomAD4 exome AF: 0.0452 AC: 44375AN: 981104Hom.: 8 Cov.: 15 AF XY: 0.0456 AC XY: 22063AN XY: 484220
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GnomAD4 genome AF: 0.00209 AC: 309AN: 147846Hom.: 3 Cov.: 33 AF XY: 0.00315 AC XY: 227AN XY: 72038
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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
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 18, 2024 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at