3-70956764-TTTTTTTTTTA-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001349338.3(FOXP1):c.*2473_*2482del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.0024 (1 hom., cov: 0)
  • Exomes 𝑓: 0.000062 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FOXP1 NM_001349338.3 3_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.504

Genes affected

FOXP1 (HGNC:3823): (forkhead box P1) This gene belongs to subfamily P of the forkhead box (FOX) transcription factor family. Forkhead box transcription factors play important roles in the regulation of tissue- and cell type-specific gene transcription during both development and adulthood. Forkhead box P1 protein contains both DNA-binding- and protein-protein binding-domains. This gene may act as a tumor suppressor as it is lost in several tumor types and maps to a chromosomal region (3p14.1) reported to contain a tumor suppressor gene(s). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOXP1	NM_001349338.3	c.*2473_*2482del		3_prime_UTR_variant	21/21	ENST00000649528.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOXP1	ENST00000649528.3	c.*2473_*2482del		3_prime_UTR_variant	21/21		NM_001349338.3	P4
FOXP1	ENST00000318789.11	c.*2473_*2482del		3_prime_UTR_variant	21/21	1		P4
FOXP1	ENST00000615603.5	n.4938_4947del		non_coding_transcript_exon_variant	20/20	5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 303 AN: 126882 Hom.: 1 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.000900

Gnomad AMI AF: 0.0140

Gnomad AMR AF: 0.000729

Gnomad ASJ AF: 0.00122

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000513

Gnomad FIN AF: 0.000260

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00391

Gnomad OTH AF: 0.00236

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000624 AC: 4 AN: 64130 Hom.: 0 AF XY: 0.0000330 AC XY: 1 AN XY: 30294

Gnomad4 AFR exome AF: 0.000411

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: 0.0000751

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00239 AC: 303 AN: 126958 Hom.: 1 Cov.: 0 AF XY: 0.00188 AC XY: 115 AN XY: 61288

Gnomad4 AFR AF: 0.000897

Gnomad4 AMR AF: 0.000727

Gnomad4 ASJ AF: 0.00122

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000515

Gnomad4 FIN AF: 0.000260

Gnomad4 NFE AF: 0.00391

Gnomad4 OTH AF: 0.00233

Alfa AF: 0.00135 Hom.: 0

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Intellectual Disability with Language Impairment and Autistic Features Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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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: rs886058837; hg19: chr3-71005915;