rs782180627

Variant names:

• chrX-49264991-C-A
• ENST00000703450.1:c.-23+1144G>T

Your query was ambiguous. Multiple possible variants found:

• chrX-49264991-C-A
• chrX-49264991-C-G

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4

The ENST00000703450.1(ENSG00000290184):​c.-23+1144G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: 20)
  • Exomes 𝑓: 0.0000016 (0 hom. 0 hem.)
• Consequence: ENSG00000290184 ENST00000703450.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.30

Genes affected

ENSG00000290184 (HGNC:):

ENSG00000286181 (HGNC:53589): (FOXP3 regulating long intergenic non-coding RNA)

FOXP3 (HGNC:6106): (forkhead box P3) The protein encoded by this gene is a member of the forkhead/winged-helix family of transcriptional regulators. Defects in this gene are the cause of immunodeficiency polyendocrinopathy, enteropathy, X-linked syndrome (IPEX), also known as X-linked autoimmunity-immunodeficiency syndrome. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -1 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.16).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290184	ENST00000703450.1	c.-23+1144G>T		intron_variant	Intron 3 of 3			ENSP00000515301.1
ENSG00000286181	ENST00000651462.1	n.1655G>T		non_coding_transcript_exon_variant	Exon 3 of 3
FOXP3	ENST00000376199.7	c.-353G>T		upstream_gene_variant		2		ENSP00000365372.2

Frequencies

GnomAD3 genomes Cov.: 20

GnomAD4 exome AF: 0.00000164 AC: 1 AN: 609717 Hom.: 0 Cov.: 11 AF XY: 0.00 AC XY: 0 AN XY: 163401

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000179

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 20

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.16
CADD	Benign	18
DANN	Benign	0.71

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-49121453;