16-86569101-A-T

Variant names:

• chr16-86569101-A-T
• rs1035550
• NM_005251.3:c.*260A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005251.3(FOXC2):​c.*260A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FOXC2 NM_005251.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 13 publications found

Genes affected

FOXC2 (HGNC:3801): (forkhead box C2) 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 may play a role in the development of mesenchymal tissues. [provided by RefSeq, Jul 2008]

FOXC2-AS1 (HGNC:50665): (FOXC2 antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005251.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOXC2	NM_005251.3	MANE Select	c.*260A>T		3_prime_UTR	Exon 1 of 1	NP_005242.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOXC2	ENST00000649859.1	MANE Select	c.*260A>T		3_prime_UTR	Exon 1 of 1	ENSP00000497759.1
	FOXC2-AS1	ENST00000809048.1		n.-82T>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 429910 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 225536

African (AFR) AF: 0.00 AC: 0 AN: 11732

American (AMR) AF: 0.00 AC: 0 AN: 17670

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12750

East Asian (EAS) AF: 0.00 AC: 0 AN: 28122

South Asian (SAS) AF: 0.00 AC: 0 AN: 44424

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40740

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1800

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 248596

Other (OTH) AF: 0.00 AC: 0 AN: 24076

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.92
DANN	Benign	0.62
PhyloP100		0.10

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

Other links and lift over

dbSNP: rs1035550; hg19: chr16-86602707;