rs4843162

chr16-86565798-A-Gchr16-86565798-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_125795.1(FOXC2-AS1):n.146-480T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,186 control chromosomes in the GnomAD database, including 1,345 homozygotes. 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: 𝑓 0.12 (1345 hom., cov: 33)
• Consequence: FOXC2-AS1 NR_125795.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOXC2-AS1	NR_125795.1	n.146-480T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOXC2-AS1	ENST00000563280.3	n.232-480T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17818 AN: 152070 Hom.: 1338 Cov.: 33

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.0925

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.0821

Gnomad FIN AF: 0.0756

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0718

Gnomad OTH AF: 0.0980

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.117 AC: 17859 AN: 152186 Hom.: 1345 Cov.: 33 AF XY: 0.116 AC XY: 8635 AN XY: 74398

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.0925

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.0820

Gnomad4 FIN AF: 0.0756

Gnomad4 NFE AF: 0.0718

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0384 Hom.: 24

Bravo AF: 0.127

Asia WGS AF: 0.152 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.1
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4843162; hg19: chr16-86599404;