chr19-46746070-T-TGGCGGCGGC
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_024301.5(FKRP):c.-266_-258dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000386 in 1,216,554 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00014 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000024 ( 0 hom. )
Consequence
FKRP
NM_024301.5 5_prime_UTR
NM_024301.5 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.763
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]
Genome browser will be placed here
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-T-TGGCGGCGGC is Benign according to our data. Variant chr19-46746070-T-TGGCGGCGGC is described in ClinVar as [Likely_benign]. Clinvar id is 420683.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| FKRP | NM_024301.5 | c.-266_-258dup | 5_prime_UTR_variant | 1/4 | ENST00000318584.10 | ||
| STRN4 | NM_013403.3 | c.282+78_282+79insGCCGCCGCC | intron_variant | ENST00000263280.11 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FKRP | ENST00000318584.10 | c.-266_-258dup | 5_prime_UTR_variant | 1/4 | 1 | NM_024301.5 | P1 | ||
| STRN4 | ENST00000263280.11 | c.282+78_282+79insGCCGCCGCC | intron_variant | 1 | NM_013403.3 | P4 |
Frequencies
GnomAD3 genomes 0.000140 AC: 21AN: 150254Hom.: 0 Cov.: 30
GnomAD3 genomes
AF:
AC:
21
AN:
150254
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000244 AC: 26AN: 1066192Hom.: 0 Cov.: 26 AF XY: 0.0000231 AC XY: 12AN XY: 518542
GnomAD4 exome
AF:
AC:
26
AN:
1066192
Hom.:
Cov.:
26
AF XY:
AC XY:
12
AN XY:
518542
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome 0.000140 AC: 21AN: 150362Hom.: 0 Cov.: 30 AF XY: 0.000136 AC XY: 10AN XY: 73440
GnomAD4 genome
AF:
AC:
21
AN:
150362
Hom.:
Cov.:
30
AF XY:
AC XY:
10
AN XY:
73440
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
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 | Apr 24, 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. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at