6-1610015-GCCC-GCCCCCC

Variant names:

• chr6-1610015-G-GCCC
• rs562673925
• NM_001453.3:c.-419_-417dupCCC

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001453.3(FOXC1):​c.-419_-417dupCCC 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 0.036 (21 hom., cov: 13)
  • Exomes 𝑓: 0.0078 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FOXC1 NM_001453.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

Genes affected

FOXC1 (HGNC:3800): (forkhead box C1) This gene belongs to the forkhead family of transcription factors which is characterized by a distinct DNA-binding forkhead domain. The specific function of this gene has not yet been determined; however, it has been shown to play a role in the regulation of embryonic and ocular development. Mutations in this gene cause various glaucoma phenotypes including primary congenital glaucoma, autosomal dominant iridogoniodysgenesis anomaly, and Axenfeld-Rieger anomaly. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXC1	NM_001453.3	c.-419_-417dupCCC		5_prime_UTR_variant	Exon 1 of 1	ENST00000645831.2	NP_001444.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXC1	ENST00000645831	c.-419_-417dupCCC		5_prime_UTR_variant	Exon 1 of 1		NM_001453.3	ENSP00000493906.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 3303 AN: 92552 Hom.: 21 Cov.: 13 FAILED QC

Gnomad AFR AF: 0.0366

Gnomad AMI AF: 0.0187

Gnomad AMR AF: 0.0258

Gnomad ASJ AF: 0.0393

Gnomad EAS AF: 0.0185

Gnomad SAS AF: 0.0173

Gnomad FIN AF: 0.0147

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0416

Gnomad OTH AF: 0.0329

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00781 AC: 1 AN: 128 Hom.: 0 Cov.: 0 AF XY: 0.0106 AC XY: 1 AN XY: 94

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00909

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0357 AC: 3304 AN: 92546 Hom.: 21 Cov.: 13 AF XY: 0.0340 AC XY: 1474 AN XY: 43394

Gnomad4 AFR AF: 0.0365

Gnomad4 AMR AF: 0.0258

Gnomad4 ASJ AF: 0.0393

Gnomad4 EAS AF: 0.0185

Gnomad4 SAS AF: 0.0174

Gnomad4 FIN AF: 0.0147

Gnomad4 NFE AF: 0.0417

Gnomad4 OTH AF: 0.0327

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: rs562673925; hg19: chr6-1610250;