X-147944810-ACC-AC
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_002024.6(FMR1):c.1472-56delC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. There are indicators that this mutation may affect the branch point..
Frequency
Genomes: 𝑓 1.0 ( 38552 hom., 25601 hem., cov: 0)
Exomes 𝑓: 1.0 ( 357435 hom. 337010 hem. )
Failed GnomAD Quality Control
Consequence
FMR1
NM_002024.6 intron
NM_002024.6 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.233
Publications
3 publications found
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]
FMR1 Gene-Disease associations (from GenCC):
- fragile X syndromeInheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Myriad Women’s Health, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics
- fragile X-associated tremor/ataxia syndromeInheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, G2P, Ambry Genetics
- premature ovarian failure 1Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- symptomatic form of fragile X syndrome in female carrierInheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 1.00 AC: 102698AN: 102703Hom.: 38557 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
102698
AN:
102703
Hom.:
Cov.:
0
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 Data not reliable, filtered out with message: InbreedingCoeff AF: 0.999 AC: 1052801AN: 1053725Hom.: 357435 Cov.: 0 AF XY: 1.00 AC XY: 337010AN XY: 337011 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
AC:
1052801
AN:
1053725
Hom.:
Cov.:
0
AF XY:
AC XY:
337010
AN XY:
337011
show subpopulations
African (AFR)
AF:
AC:
24473
AN:
24506
American (AMR)
AF:
AC:
30186
AN:
30263
Ashkenazi Jewish (ASJ)
AF:
AC:
18077
AN:
18101
East Asian (EAS)
AF:
AC:
29380
AN:
29411
South Asian (SAS)
AF:
AC:
48491
AN:
48547
European-Finnish (FIN)
AF:
AC:
37601
AN:
37655
Middle Eastern (MID)
AF:
AC:
2910
AN:
2916
European-Non Finnish (NFE)
AF:
AC:
817733
AN:
818338
Other (OTH)
AF:
AC:
43950
AN:
43988
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.840
Heterozygous variant carriers
0
96
193
289
386
482
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 1.00 AC: 102710AN: 102715Hom.: 38552 Cov.: 0 AF XY: 1.00 AC XY: 25601AN XY: 25601 show subpopulations
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
AC:
102710
AN:
102715
Hom.:
Cov.:
0
AF XY:
AC XY:
25601
AN XY:
25601
show subpopulations
African (AFR)
AF:
AC:
28142
AN:
28143
American (AMR)
AF:
AC:
9387
AN:
9387
Ashkenazi Jewish (ASJ)
AF:
AC:
2524
AN:
2524
East Asian (EAS)
AF:
AC:
3194
AN:
3194
South Asian (SAS)
AF:
AC:
2069
AN:
2069
European-Finnish (FIN)
AF:
AC:
4161
AN:
4164
Middle Eastern (MID)
AF:
AC:
198
AN:
198
European-Non Finnish (NFE)
AF:
AC:
50992
AN:
50993
Other (OTH)
AF:
AC:
1379
AN:
1379
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.835
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Asia WGS
AF:
AC:
2430
AN:
2438
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
La Branchor
BranchPoint Hunter
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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