rs4843162

Variant names:

• chr16-86565798-A-G
• rs4843162
• ENST00000809053.1:n.258T>C

Your query was ambiguous. Multiple possible variants found:

• chr16-86565798-A-G
• chr16-86565798-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000809053.1(FOXC2-AS1):​n.258T>C variant causes a non coding transcript exon 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 ENST00000809053.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FOXC2-AS1	NR_125795.1	n.146-480T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXC2-AS1	ENST00000809053.1	n.258T>C		non_coding_transcript_exon_variant	Exon 3 of 3
FOXC2-AS1	ENST00000563280.4	n.314-480T>C		intron_variant	Intron 1 of 1	3
FOXC2-AS1	ENST00000809048.1	n.63-480T>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.189 AC: 7862 AN: 41514

American (AMR) AF: 0.132 AC: 2026 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0925 AC: 321 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1189 AN: 5142

South Asian (SAS) AF: 0.0820 AC: 396 AN: 4832

European-Finnish (FIN) AF: 0.0756 AC: 802 AN: 10612

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0718 AC: 4881 AN: 68000

Other (OTH) AF: 0.102 AC: 215 AN: 2114

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
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs4843162; hg19: chr16-86599404;