6-1610015-GC-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001453.3(FOXC1):c.-417del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.063 (72 hom., cov: 13)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FOXC1 NM_001453.3 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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 Likely_benign. Variant got -2 ACMG points.

• BP6: Variant 6-1610015-GC-G is Benign according to our data. Variant chr6-1610015-GC-G is described in ClinVar as [Benign]. Clinvar id is 1220557.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOXC1	NM_001453.3	c.-417del		5_prime_UTR_variant	1/1	ENST00000645831.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOXC1	ENST00000645831.2	c.-417del		5_prime_UTR_variant	1/1		NM_001453.3	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 5845 AN: 92366 Hom.: 72 Cov.: 13 FAILED QC

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.0168

Gnomad AMR AF: 0.0530

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0225

Gnomad SAS AF: 0.0421

Gnomad FIN AF: 0.0206

Gnomad MID AF: 0.0163

Gnomad NFE AF: 0.0585

Gnomad OTH AF: 0.0563

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 128 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 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: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0633 AC: 5851 AN: 92360 Hom.: 72 Cov.: 13 AF XY: 0.0613 AC XY: 2657 AN XY: 43320

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.0528

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.0226

Gnomad4 SAS AF: 0.0421

Gnomad4 FIN AF: 0.0206

Gnomad4 NFE AF: 0.0585

Gnomad4 OTH AF: 0.0559

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 16, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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;