10-93702522-A-ACCGCCG

Position:

• chr10-93702522-A-ACCGCCG

Variant summary

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

The NM_145246.5(FRA10AC1):​c.-154_-149dupCGGCGG 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 0.0017 (1 hom., cov: 0)
  • Exomes 𝑓: 0.0022 (40 hom.)
• Consequence: FRA10AC1 NM_145246.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FRA10AC1	NM_145246.5	c.-154_-149dupCGGCGG		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	c.-154_-149dupCGGCGG		5_prime_UTR_variant	1/14	1	NM_145246.5	ENSP00000360488.3

Frequencies

GnomAD3 genomes AF: 0.00174 AC: 257 AN: 147318 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.00351

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00161

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.00240

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000105

Gnomad OTH AF: 0.00199

GnomAD4 exome AF: 0.00222 AC: 152 AN: 68608 Hom.: 40 Cov.: 0 AF XY: 0.00173 AC XY: 74 AN XY: 42850

Gnomad4 AFR exome AF: 0.00196

Gnomad4 AMR exome AF: 0.00484

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0880

Gnomad4 SAS exome AF: 0.000726

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000224

Gnomad4 OTH exome AF: 0.00416

GnomAD4 genome AF: 0.00175 AC: 258 AN: 147434 Hom.: 1 Cov.: 0 AF XY: 0.00188 AC XY: 135 AN XY: 71842

Gnomad4 AFR AF: 0.00355

Gnomad4 AMR AF: 0.00161

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0140

Gnomad4 SAS AF: 0.00240

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000105

Gnomad4 OTH AF: 0.00197

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs139811637; hg19: chr10-95462279;