NM_001349338.3:c.*3403_*3414dupTGTGTGTGTGTG

Variant summary

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

The NM_001349338.3(FOXP1):​c.*3403_*3414dupTGTGTGTGTGTG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00838 in 221,482 control chromosomes in the GnomAD database, including 15 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0063 ( 15 hom., cov: 26)
Exomes 𝑓: 0.012 ( 0 hom. )

Consequence

FOXP1
NM_001349338.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.373
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0833 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FOXP1NM_001349338.3 linkc.*3403_*3414dupTGTGTGTGTGTG 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
FOXP1ENST00000649528 linkc.*3403_*3414dupTGTGTGTGTGTG 3_prime_UTR_variant Exon 21 of 21 NM_001349338.3 ENSP00000497369.1 Q9H334-1
FOXP1ENST00000318789 linkc.*3403_*3414dupTGTGTGTGTGTG 3_prime_UTR_variant Exon 21 of 21 1 ENSP00000318902.5 Q9H334-1

Frequencies

GnomAD3 genomes
AF:
0.00630
AC:
927
AN:
147164
Hom.:
15
Cov.:
26
show subpopulations
Gnomad AFR
AF:
0.00730
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00219
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0901
Gnomad SAS
AF:
0.00967
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00962
Gnomad NFE
AF:
0.00139
Gnomad OTH
AF:
0.00395
GnomAD4 exome
AF:
0.0125
AC:
925
AN:
74222
Hom.:
0
Cov.:
0
AF XY:
0.0125
AC XY:
427
AN XY:
34094
show subpopulations
Gnomad4 AFR exome
AF:
0.00525
Gnomad4 AMR exome
AF:
0.000873
Gnomad4 ASJ exome
AF:
0.000215
Gnomad4 EAS exome
AF:
0.0723
Gnomad4 SAS exome
AF:
0.00704
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00145
Gnomad4 OTH exome
AF:
0.00652
GnomAD4 genome
AF:
0.00632
AC:
931
AN:
147260
Hom.:
15
Cov.:
26
AF XY:
0.00679
AC XY:
486
AN XY:
71620
show subpopulations
Gnomad4 AFR
AF:
0.00728
Gnomad4 AMR
AF:
0.00218
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0901
Gnomad4 SAS
AF:
0.0106
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00139
Gnomad4 OTH
AF:
0.00440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs143202281; hg19: chr3-71004983; API