X-49264512-ATT-ATTTTT

Variant names:

• chrX-49264512-A-ATTT
• rs35302628
• NM_014009.4:c.-23+146_-23+148dupAAA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP6_Moderate

The NM_014009.4(FOXP3):​c.-23+146_-23+148dupAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: FOXP3 NM_014009.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.260
• Publications: 0 publications found

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]

ENSG00000290184 (HGNC:):

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

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant X-49264512-A-ATTT is Benign according to our data. Variant chrX-49264512-A-ATTT is described in CliVar as Benign. Clinvar id is 2688118.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-49264512-A-ATTT is described in CliVar as Benign. Clinvar id is 2688118.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-49264512-A-ATTT is described in CliVar as Benign. Clinvar id is 2688118.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-49264512-A-ATTT is described in CliVar as Benign. Clinvar id is 2688118.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-49264512-A-ATTT is described in CliVar as Benign. Clinvar id is 2688118.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-49264512-A-ATTT is described in CliVar as Benign. Clinvar id is 2688118.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-49264512-A-ATTT is described in CliVar as Benign. Clinvar id is 2688118.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-49264512-A-ATTT is described in CliVar as Benign. Clinvar id is 2688118.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-49264512-A-ATTT is described in CliVar as Benign. Clinvar id is 2688118.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXP3	NM_014009.4	c.-23+146_-23+148dupAAA		intron_variant	Intron 1 of 11	ENST00000376207.10	NP_054728.2
FOXP3	NM_001114377.2	c.-23+146_-23+148dupAAA		intron_variant	Intron 1 of 10		NP_001107849.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXP3	ENST00000376207.10	c.-23+146_-23+148dupAAA		intron_variant	Intron 1 of 11	1	NM_014009.4	ENSP00000365380.4
ENSG00000290184	ENST00000703450.1	c.-23+1620_-23+1622dupAAA		intron_variant	Intron 3 of 3			ENSP00000515301.1

Frequencies

GnomAD3 genomes Cov.: 23

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

GnomAD4 genome Cov.: 23

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Jan 24, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 52% of patients studied by a panel of primary immunodeficiencies. Number of patients: 49. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs35302628; hg19: chrX-49120974;