chr19-46746070-TGGCGGC-T
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_024301.5(FKRP):c.-263_-258del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000205 in 1,216,422 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00022 ( 1 hom. )
Consequence
FKRP
NM_024301.5 5_prime_UTR
NM_024301.5 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.55
Genes affected
FKRP (HGNC:17997): (fukutin related protein) This gene encodes a protein which is targeted to the medial Golgi apparatus and is necessary for posttranslational modification of dystroglycan. Mutations in this gene have been associated with congenital muscular dystrophy, cognitive disability, and cerebellar cysts. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 19-46746070-TGGCGGC-T is Benign according to our data. Variant chr19-46746070-TGGCGGC-T is described in ClinVar as [Likely_benign]. Clinvar id is 518044.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| FKRP | NM_024301.5 | c.-263_-258del | 5_prime_UTR_variant | 1/4 | ENST00000318584.10 | NP_077277.1 | ||
| STRN4 | NM_013403.3 | c.282+73_282+78del | intron_variant | ENST00000263280.11 | NP_037535.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| FKRP | ENST00000318584.10 | c.-263_-258del | 5_prime_UTR_variant | 1/4 | 1 | NM_024301.5 | ENSP00000326570 | P1 | ||
| STRN4 | ENST00000263280.11 | c.282+73_282+78del | intron_variant | 1 | NM_013403.3 | ENSP00000263280 | P4 |
Frequencies
GnomAD3 genomes 0.000120 AC: 18AN: 150254Hom.: 0 Cov.: 30
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GnomAD4 exome AF: 0.000217 AC: 231AN: 1066168Hom.: 1 AF XY: 0.000179 AC XY: 93AN XY: 518530
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GnomAD4 genome 0.000120 AC: 18AN: 150254Hom.: 0 Cov.: 30 AF XY: 0.000109 AC XY: 8AN XY: 73320
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
| Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 21, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at