rs398123612

Variant names:

• chr6-1611782-ACGGCGGCGGCGGCGG-A
• NM_001453.3:c.1347_1361delCGGCGGCGGCGGCGG

Your query was ambiguous. Multiple possible variants found:

• chr6-1611782-ACGGCGGCGGCGGCGG-A
• chr6-1611782-ACGGCGGCGGCGGCGG-ACGG
• chr6-1611782-ACGGCGGCGGCGGCGG-ACGGCGG
• chr6-1611782-ACGGCGGCGGCGGCGG-ACGGCGGCGG
• chr6-1611782-ACGGCGGCGGCGGCGG-ACGGCGGCGGCGG
• chr6-1611782-ACGGCGGCGGCGGCGG-ACGGCGGCGGCGGCGGCGG
• chr6-1611782-ACGGCGGCGGCGGCGG-ACGGCGGCGGCGGCGGCGGCGG
• chr6-1611782-ACGGCGGCGGCGGCGG-ACGGCGGCGGCGGCGGCGGCGGCGG
• chr6-1611782-ACGGCGGCGGCGGCGG-ACGGCGGCGGCGGCGGCGGCGGCGGCGG
• chr6-1611782-ACGGCGGCGGCGGCGG-ACGGCGGCGGCGGCGGCGGCGGCGGCGGCGG

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001453.3(FOXC1):​c.1347_1361delCGGCGGCGGCGGCGG​(p.Gly450_Gly454del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000771 in 1,297,672 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 19)
  • Exomes 𝑓: 7.7e-7 (0 hom.)
• Consequence: FOXC1 NM_001453.3 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.10

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 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXC1	NM_001453.3	c.1347_1361delCGGCGGCGGCGGCGG	p.Gly450_Gly454del	disruptive_inframe_deletion	Exon 1 of 1	ENST00000645831.2	NP_001444.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXC1	ENST00000645831.2	c.1347_1361delCGGCGGCGGCGGCGG	p.Gly450_Gly454del	disruptive_inframe_deletion	Exon 1 of 1		NM_001453.3	ENSP00000493906.1

Frequencies

GnomAD3 genomes Cov.: 19

GnomAD4 exome AF: 7.71e-7 AC: 1 AN: 1297672 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 639922

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000420

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 19

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-1612017;