NM_001349338.3:c.*3409_*3414delTGTGTG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_001349338.3(FOXP1):​c.*3409_*3414delTGTGTG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00051 in 221,612 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00041 ( 0 hom., cov: 26)
Exomes 𝑓: 0.00071 ( 0 hom. )

Consequence

FOXP1
NM_001349338.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.52
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.

BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000407 (60/147260) while in subpopulation EAS AF= 0.00299 (15/5016). AF 95% confidence interval is 0.00184. There are 0 homozygotes in gnomad4. There are 37 alleles in male gnomad4 subpopulation. Median coverage is 26. This position pass quality control queck.
BS2
High AC in GnomAd4 at 60 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FOXP1NM_001349338.3 linkc.*3409_*3414delTGTGTG 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.*3409_*3414delTGTGTG 3_prime_UTR_variant Exon 21 of 21 NM_001349338.3 ENSP00000497369.1 Q9H334-1
FOXP1ENST00000318789 linkc.*3409_*3414delTGTGTG 3_prime_UTR_variant Exon 21 of 21 1 ENSP00000318902.5 Q9H334-1

Frequencies

GnomAD3 genomes
AF:
0.000408
AC:
60
AN:
147164
Hom.:
0
Cov.:
26
show subpopulations
Gnomad AFR
AF:
0.000819
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000683
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00298
Gnomad SAS
AF:
0.000215
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000136
Gnomad OTH
AF:
0.000494
GnomAD4 exome
AF:
0.000713
AC:
53
AN:
74352
Hom.:
0
AF XY:
0.000849
AC XY:
29
AN XY:
34148
show subpopulations
Gnomad4 AFR exome
AF:
0.000262
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.000215
Gnomad4 EAS exome
AF:
0.00353
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000245
Gnomad4 OTH exome
AF:
0.000163
GnomAD4 genome
AF:
0.000407
AC:
60
AN:
147260
Hom.:
0
Cov.:
26
AF XY:
0.000517
AC XY:
37
AN XY:
71616
show subpopulations
Gnomad4 AFR
AF:
0.000817
Gnomad4 AMR
AF:
0.0000683
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00299
Gnomad4 SAS
AF:
0.000216
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000136
Gnomad4 OTH
AF:
0.000489

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