rs3060515

Variant names:

• chrX-49264507-C-CTAT
• rs3060515
• NM_014009.4:c.-23+151_-23+153dupATA

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_014009.4(FOXP3):​c.-23+151_-23+153dupATA 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
• Publications: 2 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: Likely_benign. The variant received -2 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 VariationId is 2688146.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014009.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOXP3	NM_014009.4	MANE Select	c.-23+151_-23+153dupATA		intron	N/A	NP_054728.2
	FOXP3	NM_001114377.2		c.-23+151_-23+153dupATA		intron	N/A	NP_001107849.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOXP3	ENST00000376207.10	TSL:1 MANE Select	c.-23+151_-23+153dupATA		intron	N/A	ENSP00000365380.4
	ENSG00000290184	ENST00000703450.1		c.-23+1625_-23+1627dupATA		intron	N/A	ENSP00000515301.1
	FLICR	ENST00000651462.1		n.2136_2138dupATA		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.517 AC: 56494 AN: 109361 Hom.: 10968 Cov.: 0

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

African (AFR) AF: 0.429 AC: 12877 AN: 29997

American (AMR) AF: 0.452 AC: 4697 AN: 10399

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 1555 AN: 2621

East Asian (EAS) AF: 0.379 AC: 1315 AN: 3471

South Asian (SAS) AF: 0.573 AC: 1434 AN: 2504

European-Finnish (FIN) AF: 0.470 AC: 2663 AN: 5662

Middle Eastern (MID) AF: 0.585 AC: 124 AN: 212

European-Non Finnish (NFE) AF: 0.587 AC: 30744 AN: 52400

Other (OTH) AF: 0.524 AC: 775 AN: 1479

Alfa AF: 0.525 Hom.: 3245

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs3060515; hg19: chrX-49120966;