Variant rs193922911 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000359204.5(FRA10AC1):c.-149_-148insCGG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.013 ( 48 hom., cov: 0)

Exomes 𝑓: 0.0060 ( 19 hom. )

Consequence

FRA10AC1
ENST00000359204.5 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.03

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FRA10AC1	NM_145246.5 linkuse as main transcript	c.-149_-148insCGG		5_prime_UTR_variant	1/14	ENST00000359204.5	NP_660289.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FRA10AC1	ENST00000359204.5 linkuse as main transcript	c.-149_-148insCGG		5_prime_UTR_variant	1/14	1	NM_145246.5	ENSP00000360488	P1	Q70Z53-1

Frequencies

GnomAD3 genomes

AF:

0.0126

AC:

1852

AN:

147308

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0316

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00483

Gnomad ASJ

AF:

0.00294

Gnomad EAS

AF:

0.0723

Gnomad SAS

AF:

0.00741

Gnomad FIN

AF:

0.000505

Gnomad MID

AF:

0.00662

Gnomad NFE

AF:

0.00137

Gnomad OTH

AF:

0.00748

GnomAD4 exome

AF:

0.00598

AC:

410

AN:

68588

Hom.:

Cov.:

AF XY:

0.00658

AC XY:

282

AN XY:

42832

show subpopulations

Gnomad4 AFR exome

AF:

0.0285

Gnomad4 AMR exome

AF:

0.00823

Gnomad4 ASJ exome

AF:

0.00102

Gnomad4 EAS exome

AF:

0.0762

Gnomad4 SAS exome

AF:

0.00992

Gnomad4 FIN exome

AF:

0.00144

Gnomad4 NFE exome

AF:

0.00229

Gnomad4 OTH exome

AF:

0.0128

GnomAD4 genome

AF:

0.0126

AC:

1853

AN:

147424

Hom.:

Cov.:

AF XY:

0.0128

AC XY:

917

AN XY:

71838

show subpopulations

Gnomad4 AFR

AF:

0.0316

Gnomad4 AMR

AF:

0.00483

Gnomad4 ASJ

AF:

0.00294

Gnomad4 EAS

AF:

0.0719

Gnomad4 SAS

AF:

0.00742

Gnomad4 FIN

AF:

0.000505

Gnomad4 NFE

AF:

0.00137

Gnomad4 OTH

AF:

0.00740

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over