GeneBe

rs139811637

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_145246.5(FRA10AC1):​c.-166_-149delCGGCGGCGGCGGCGGCGG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000068 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

FRA10AC1
NM_145246.5 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.08

Publications

1 publications found
Variant links:
Genes affected
FRA10AC1 (HGNC:1162): (FRA10A associated CGG repeat 1) The protein encoded by this gene is a nuclear phosphoprotein of unknown function. This gene contains a tandem CGG repeat region within a CpG island that normally consists of 8-14 repeats but can expand to over 200 repeats. The repeat region is within the 5' UTR of some transcript variants, but is intronic to another variant. The expanded repeat allele is a fragile site and becomes hypermethylated, causing a reduction in gene expression. A disease phenotype has not been associated with expanded alleles. This gene is found within the rare FRA10A folate-sensitive fragile site. [provided by RefSeq, Dec 2016]
FRA10AC1 Gene-Disease associations (from GenCC):
  • neurodevelopmental disorder with growth retardation, dysmorphic facies, and corpus callosum abnormalities
    Inheritance: AR Classification: STRONG, MODERATE Submitted by: Ambry Genetics, G2P

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145246.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
FRA10AC1
NM_145246.5
MANE Select
c.-166_-149delCGGCGGCGGCGGCGGCGG
5_prime_UTR
Exon 1 of 14NP_660289.2
FRA10AC1
NM_001347712.2
c.-367_-350delCGGCGGCGGCGGCGGCGG
5_prime_UTR
Exon 1 of 14NP_001334641.1Q70Z53-1
FRA10AC1
NM_001347713.2
c.-286_-269delCGGCGGCGGCGGCGGCGG
5_prime_UTR
Exon 1 of 15NP_001334642.1Q70Z53-1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
FRA10AC1
ENST00000359204.5
TSL:1 MANE Select
c.-166_-149delCGGCGGCGGCGGCGGCGG
5_prime_UTR
Exon 1 of 14ENSP00000360488.3Q70Z53-1
FRA10AC1
ENST00000959343.1
c.-166_-149delCGGCGGCGGCGGCGGCGG
5_prime_UTR
Exon 1 of 14ENSP00000629402.1
FRA10AC1
ENST00000905754.1
c.-367_-350delCGGCGGCGGCGGCGGCGG
5_prime_UTR
Exon 1 of 14ENSP00000575813.1

Frequencies

GnomAD3 genomes
AF:
0.00000679
AC:
1
AN:
147320
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000151
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
68612
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
42852
African (AFR)
AF:
0.00
AC:
0
AN:
1018
American (AMR)
AF:
0.00
AC:
0
AN:
2066
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
976
East Asian (EAS)
AF:
0.00
AC:
0
AN:
1206
South Asian (SAS)
AF:
0.00
AC:
0
AN:
12402
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
2786
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
228
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
44562
Other (OTH)
AF:
0.00
AC:
0
AN:
3368
GnomAD4 genome
AF:
0.00000679
AC:
1
AN:
147320
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
71720
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
39890
American (AMR)
AF:
0.00
AC:
0
AN:
14892
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3396
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5022
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4586
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
9900
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
302
European-Non Finnish (NFE)
AF:
0.0000151
AC:
1
AN:
66422
Other (OTH)
AF:
0.00
AC:
0
AN:
2006
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.825
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
649

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs139811637; hg19: chr10-95462279; API