GeneBe

rs143202281

Variant names:

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The NM_001349338.3(FOXP1):​c.*3405_*3414delTGTGTGTGTG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 221,538 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 0.000020 ( 0 hom., cov: 26)
Exomes 𝑓: 0.000054 ( 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 Likely_benign. Variant got -4 ACMG points.

BS1
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.0000538 (4/74370) while in subpopulation NFE AF= 0.000089 (4/44954). AF 95% confidence interval is 0.0000297. There are 0 homozygotes in gnomad4_exome. There are 2 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FOXP1NM_001349338.3 linkc.*3405_*3414delTGTGTGTGTG 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.*3405_*3414delTGTGTGTGTG 3_prime_UTR_variant Exon 21 of 21 NM_001349338.3 ENSP00000497369.1 Q9H334-1
FOXP1ENST00000318789 linkc.*3405_*3414delTGTGTGTGTG 3_prime_UTR_variant Exon 21 of 21 1 ENSP00000318902.5 Q9H334-1

Frequencies

GnomAD3 genomes
AF:
0.0000204
AC:
3
AN:
147168
Hom.:
0
Cov.:
26
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000215
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000301
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000538
AC:
4
AN:
74370
Hom.:
0
AF XY:
0.0000585
AC XY:
2
AN XY:
34160
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000890
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000204
AC:
3
AN:
147168
Hom.:
0
Cov.:
26
AF XY:
0.0000280
AC XY:
2
AN XY:
71512
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000215
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000301
Gnomad4 OTH
AF:
0.00

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