rs25726
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002024.6(FMR1):c.52-112A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 504,986 control chromosomes in the GnomAD database, including 3,346 homozygotes. There are 22,788 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.13 ( 720 hom., 4022 hem., cov: 23)
Exomes 𝑓: 0.14 ( 2626 hom. 18766 hem. )
Consequence
FMR1
NM_002024.6 intron
NM_002024.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0640
Genes affected
FMR1 (HGNC:3775): (fragile X messenger ribonucleoprotein 1) The protein encoded by this gene binds RNA and is associated with polysomes. The encoded protein may be involved in mRNA trafficking from the nucleus to the cytoplasm. A trinucleotide repeat (CGG) in the 5' UTR is normally found at 6-53 copies, but an expansion to 55-230 repeats is the cause of fragile X syndrome. Expansion of the trinucleotide repeat may also cause one form of premature ovarian failure (POF1). Multiple alternatively spliced transcript variants that encode different protein isoforms and which are located in different cellular locations have been described for this gene. [provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant X-147921821-A-G is Benign according to our data. Variant chrX-147921821-A-G is described in ClinVar as [Benign]. Clinvar id is 1224679.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FMR1 | NM_002024.6 | c.52-112A>G | intron_variant | ENST00000370475.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FMR1 | ENST00000370475.9 | c.52-112A>G | intron_variant | 1 | NM_002024.6 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.126 AC: 14096AN: 111665Hom.: 718 Cov.: 23 AF XY: 0.118 AC XY: 4008AN XY: 33887
GnomAD3 genomes
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GnomAD4 exome AF: 0.138 AC: 54454AN: 393269Hom.: 2626 AF XY: 0.147 AC XY: 18766AN XY: 127999
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GnomAD4 genome ? AF: 0.126 AC: 14105AN: 111717Hom.: 720 Cov.: 23 AF XY: 0.118 AC XY: 4022AN XY: 33949
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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 | GeneDx | Nov 11, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at