ENST00000743607.1:n.456-678A>C

Variant names:

• chr14-28725066-T-G
• rs1955449
• ENST00000743607.1:n.456-678A>C

Variant summary

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

The ENST00000743607.1(FOXG1-AS1):​n.456-678A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,782 control chromosomes in the GnomAD database, including 14,387 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 0.42 (14387 hom., cov: 30)
• Consequence: FOXG1-AS1 ENST00000743607.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120
• Publications: 2 publications found

Genes affected

FOXG1-AS1 (HGNC:50663): (FOXG1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXG1-AS1	NR_125758.1	n.*176A>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXG1-AS1	ENST00000743607.1	n.456-678A>C		intron_variant	Intron 4 of 4
FOXG1-AS1	ENST00000743608.1	n.750+289A>C		intron_variant	Intron 8 of 8
FOXG1-AS1	ENST00000743621.1	n.143-678A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63881 AN: 151664 Hom.: 14390 Cov.: 30

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.421 AC: 63891 AN: 151782 Hom.: 14387 Cov.: 30 AF XY: 0.425 AC XY: 31504 AN XY: 74164

African (AFR) AF: 0.293 AC: 12146 AN: 41426

American (AMR) AF: 0.369 AC: 5613 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1243 AN: 3472

East Asian (EAS) AF: 0.826 AC: 4259 AN: 5154

South Asian (SAS) AF: 0.468 AC: 2253 AN: 4816

European-Finnish (FIN) AF: 0.518 AC: 5437 AN: 10506

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31252 AN: 67876

Other (OTH) AF: 0.425 AC: 895 AN: 2108

Alfa AF: 0.280 Hom.: 713

Bravo AF: 0.410

Asia WGS AF: 0.599 AC: 2080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.74
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1955449; hg19: chr14-29194272;