chr3-70955832-G-GCACACA

Variant names:

• chr3-70955832-G-GCACACA
• rs143202281
• NM_001349338.3:c.*3409_*3414dupTGTGTG

Variant summary

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

The NM_001349338.3(FOXP1):​c.*3409_*3414dupTGTGTG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0419 in 221,474 control chromosomes in the GnomAD database, including 683 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.056 (680 hom., cov: 26)
  • Exomes 𝑓: 0.014 (3 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 (AFR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXP1	NM_001349338.3	c.*3409_*3414dupTGTGTG		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.*3409_*3414dupTGTGTG		3_prime_UTR_variant	Exon 21 of 21		NM_001349338.3	ENSP00000497369.1
FOXP1	ENST00000318789	c.*3409_*3414dupTGTGTG		3_prime_UTR_variant	Exon 21 of 21	1		ENSP00000318902.5

Frequencies

GnomAD3 genomes AF: 0.0559 AC: 8227 AN: 147108 Hom.: 678 Cov.: 26

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0269

Gnomad AMR AF: 0.0225

Gnomad ASJ AF: 0.00147

Gnomad EAS AF: 0.00835

Gnomad SAS AF: 0.00322

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.00962

Gnomad NFE AF: 0.00167

Gnomad OTH AF: 0.0440

GnomAD4 exome AF: 0.0137 AC: 1015 AN: 74272 Hom.: 3 Cov.: 0 AF XY: 0.0125 AC XY: 425 AN XY: 34114

Gnomad4 AFR exome AF: 0.177

Gnomad4 AMR exome AF: 0.0214

Gnomad4 ASJ exome AF: 0.00129

Gnomad4 EAS exome AF: 0.00309

Gnomad4 SAS exome AF: 0.00843

Gnomad4 FIN exome AF: 0.00949

Gnomad4 NFE exome AF: 0.00180

Gnomad4 OTH exome AF: 0.0267

GnomAD4 genome AF: 0.0561 AC: 8254 AN: 147202 Hom.: 680 Cov.: 26 AF XY: 0.0540 AC XY: 3867 AN XY: 71586

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.0224

Gnomad4 ASJ AF: 0.00147

Gnomad4 EAS AF: 0.00857

Gnomad4 SAS AF: 0.00302

Gnomad4 FIN AF: 0.0101

Gnomad4 NFE AF: 0.00167

Gnomad4 OTH AF: 0.0435

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;