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GeneBe

3-70955524-GA-G

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BS1_SupportingBS2

The NM_001349338.3(FOXP1):c.*3722del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000621 in 225,478 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000048 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000089 ( 0 hom. )

Consequence

FOXP1
NM_001349338.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.909
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0000476 (7/146970) while in subpopulation EAS AF= 0.0004 (2/4998). AF 95% confidence interval is 0.0000706. There are 0 homozygotes in gnomad4. There are 2 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High AC in GnomAd at 7 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FOXP1NM_001349338.3 linkuse as main transcriptc.*3722del 3_prime_UTR_variant 21/21 ENST00000649528.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FOXP1ENST00000649528.3 linkuse as main transcriptc.*3722del 3_prime_UTR_variant 21/21 NM_001349338.3 P4Q9H334-1
FOXP1ENST00000318789.11 linkuse as main transcriptc.*3722del 3_prime_UTR_variant 21/211 P4Q9H334-1

Frequencies

GnomAD3 genomes
AF:
0.0000476
AC:
7
AN:
146926
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000100
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000672
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000399
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000892
AC:
7
AN:
78508
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
36142
show subpopulations
Gnomad4 AFR exome
AF:
0.000266
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000905
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000618
Gnomad4 OTH exome
AF:
0.000304
GnomAD4 genome
AF:
0.0000476
AC:
7
AN:
146970
Hom.:
0
Cov.:
32
AF XY:
0.0000280
AC XY:
2
AN XY:
71398
show subpopulations
Gnomad4 AFR
AF:
0.0000998
Gnomad4 AMR
AF:
0.0000672
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000400
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000264

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Intellectual Disability with Language Impairment and Autistic Features Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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

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

Other links and lift over

dbSNP: rs886058821; hg19: chr3-71004675; API