10-93692698-G-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_145246.5(FRA10AC1):c.328C>A(p.Arg110Arg) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000833 in 1,439,890 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000083 ( 0 hom. )
Consequence
FRA10AC1
NM_145246.5 synonymous
NM_145246.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.71
Publications
0 publications found
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 abnormalitiesInheritance: AR Classification: STRONG, MODERATE Submitted by: G2P, Ambry Genetics
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 0.00000833 AC: 12AN: 1439890Hom.: 0 Cov.: 28 AF XY: 0.0000112 AC XY: 8AN XY: 716368 show subpopulations
GnomAD4 exome
AF:
AC:
12
AN:
1439890
Hom.:
Cov.:
28
AF XY:
AC XY:
8
AN XY:
716368
show subpopulations
African (AFR)
AF:
AC:
0
AN:
31922
American (AMR)
AF:
AC:
0
AN:
40276
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25682
East Asian (EAS)
AF:
AC:
0
AN:
37962
South Asian (SAS)
AF:
AC:
0
AN:
82604
European-Finnish (FIN)
AF:
AC:
0
AN:
53148
Middle Eastern (MID)
AF:
AC:
0
AN:
5730
European-Non Finnish (NFE)
AF:
AC:
11
AN:
1103050
Other (OTH)
AF:
AC:
1
AN:
59516
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.421
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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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