rs3060515

chrX-49264507-C-CTAT

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_014009.4(FOXP3):c.-23+153_-23+154insATA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.52 (10971 hom., 15713 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: FOXP3 NM_014009.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.695

Genes affected

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]

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant X-49264507-C-CTAT is Benign according to our data. Variant chrX-49264507-C-CTAT is described in ClinVar as [Benign]. Clinvar id is 2688146.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd at 10968 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOXP3	NM_014009.4	c.-23+153_-23+154insATA		intron_variant		ENST00000376207.10
FOXP3	NM_001114377.2	c.-23+153_-23+154insATA		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOXP3	ENST00000376207.10	c.-23+153_-23+154insATA		intron_variant		1	NM_014009.4	P1
	ENST00000651462.1	n.2138_2139insATA		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.517 AC: 56494 AN: 109361 Hom.: 10968 Cov.: 0 AF XY: 0.493 AC XY: 15668 AN XY: 31773

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.588

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.520

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.517 AC: 56534 AN: 109417 Hom.: 10971 Cov.: 0 AF XY: 0.494 AC XY: 15713 AN XY: 31839

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.524

Alfa AF: 0.525 Hom.: 3245

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 45% of patients studied by a panel of primary immunodeficiencies. Number of patients: 43. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3060515; hg19: chrX-49120966;