chr19-46756017-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6BP7BS1BS2_Supporting
The NM_024301.5(FKRP):c.567C>T(p.Pro189Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000303 in 1,572,228 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_024301.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FKRP | NM_024301.5 | c.567C>T | p.Pro189Pro | synonymous_variant | Exon 4 of 4 | ENST00000318584.10 | NP_077277.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00134 AC: 203AN: 151858Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000334 AC: 61AN: 182622Hom.: 0 AF XY: 0.000275 AC XY: 28AN XY: 101966
GnomAD4 exome AF: 0.000192 AC: 272AN: 1420260Hom.: 2 Cov.: 32 AF XY: 0.000176 AC XY: 124AN XY: 705172
GnomAD4 genome AF: 0.00134 AC: 204AN: 151968Hom.: 0 Cov.: 33 AF XY: 0.00131 AC XY: 97AN XY: 74306
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
This variant is associated with the following publications: (PMID: 14647208) -
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FKRP: BP4, BP7 -
not specified Benign:2
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Autosomal recessive limb-girdle muscular dystrophy type 2I Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Walker-Warburg congenital muscular dystrophy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at