NM_001349338.3:c.*2830_*2831delAA

Variant names:

• chr3-70956415-CTT-C
• rs112098084
• NM_001349338.3:c.*2830_*2831delAA

Variant summary

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

The NM_001349338.3(FOXP1):​c.*2830_*2831delAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0183 in 181,228 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00046 (1 hom., cov: 26)
  • Exomes 𝑓: 0.059 (0 hom.)
• Consequence: FOXP1 NM_001349338.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.961

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: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXP1	NM_001349338.3	c.*2830_*2831delAA		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.*2830_*2831delAA		3_prime_UTR_variant	Exon 21 of 21		NM_001349338.3	ENSP00000497369.1
FOXP1	ENST00000318789	c.*2830_*2831delAA		3_prime_UTR_variant	Exon 21 of 21	1		ENSP00000318902.5

Frequencies

GnomAD3 genomes AF: 0.000445 AC: 56 AN: 125828 Hom.: 0 Cov.: 26

Gnomad AFR AF: 0.000302

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000158

Gnomad ASJ AF: 0.00128

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000515

Gnomad FIN AF: 0.00218

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000354

Gnomad OTH AF: 0.00120

GnomAD4 exome AF: 0.0587 AC: 3253 AN: 55396 Hom.: 0 AF XY: 0.0576 AC XY: 1472 AN XY: 25554

Gnomad4 AFR exome AF: 0.0744

Gnomad4 AMR exome AF: 0.0608

Gnomad4 ASJ exome AF: 0.0524

Gnomad4 EAS exome AF: 0.0546

Gnomad4 SAS exome AF: 0.0500

Gnomad4 FIN exome AF: 0.0161

Gnomad4 NFE exome AF: 0.0600

Gnomad4 OTH exome AF: 0.0572

GnomAD4 genome AF: 0.000461 AC: 58 AN: 125832 Hom.: 1 Cov.: 26 AF XY: 0.000595 AC XY: 36 AN XY: 60482

Gnomad4 AFR AF: 0.000362

Gnomad4 AMR AF: 0.000158

Gnomad4 ASJ AF: 0.00128

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000519

Gnomad4 FIN AF: 0.00218

Gnomad4 NFE AF: 0.000354

Gnomad4 OTH AF: 0.00119

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs112098084; hg19: chr3-71005566;