NM_001349338.3:c.*3405_*3414dupTGTGTGTGTG

Variant names:

• chr3-70955832-G-GCACACACACA
• rs143202281
• NM_001349338.3:c.*3405_*3414dupTGTGTGTGTG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001349338.3(FOXP1):​c.*3405_*3414dupTGTGTGTGTG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0632 in 221,092 control chromosomes in the GnomAD database, including 512 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.067 (508 hom., cov: 26)
  • Exomes 𝑓: 0.056 (4 hom.)
• Consequence: FOXP1 NM_001349338.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373

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 Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXP1	NM_001349338.3	c.*3405_*3414dupTGTGTGTGTG		3_prime_UTR_variant	Exon 21 of 21	ENST00000649528.3	NP_001336267.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXP1	ENST00000649528	c.*3405_*3414dupTGTGTGTGTG		3_prime_UTR_variant	Exon 21 of 21		NM_001349338.3	ENSP00000497369.1
FOXP1	ENST00000318789	c.*3405_*3414dupTGTGTGTGTG		3_prime_UTR_variant	Exon 21 of 21	1		ENSP00000318902.5

Frequencies

GnomAD3 genomes AF: 0.0669 AC: 9834 AN: 147082 Hom.: 506 Cov.: 26

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0706

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.0782

Gnomad FIN AF: 0.0563

Gnomad MID AF: 0.0385

Gnomad NFE AF: 0.0216

Gnomad OTH AF: 0.0711

GnomAD4 exome AF: 0.0557 AC: 4118 AN: 73914 Hom.: 4 Cov.: 0 AF XY: 0.0550 AC XY: 1868 AN XY: 33944

Gnomad4 AFR exome AF: 0.118

Gnomad4 AMR exome AF: 0.0733

Gnomad4 ASJ exome AF: 0.0425

Gnomad4 EAS exome AF: 0.183

Gnomad4 SAS exome AF: 0.0696

Gnomad4 FIN exome AF: 0.0160

Gnomad4 NFE exome AF: 0.0217

Gnomad4 OTH exome AF: 0.0446

GnomAD4 genome AF: 0.0669 AC: 9847 AN: 147178 Hom.: 508 Cov.: 26 AF XY: 0.0685 AC XY: 4903 AN XY: 71574

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.0705

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.0787

Gnomad4 FIN AF: 0.0563

Gnomad4 NFE AF: 0.0216

Gnomad4 OTH AF: 0.0718

ClinVar

Not reported in ClinVar

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: rs143202281; hg19: chr3-71004983;