Variant 3-71053750-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate

The NM_001349338.3(FOXP1):c.306G>A(p.Met102Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,808 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

FOXP1
NM_001349338.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 7.90

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]

FOXP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP6

Variant 3-71053750-C-T is Benign according to our data. Variant chr3-71053750-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 435250.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FOXP1	NM_001349338.3 linkuse as main transcript	c.306G>A	p.Met102Ile	missense_variant	8/21	ENST00000649528.3	NP_001336267.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FOXP1	ENST00000649528.3 linkuse as main transcript	c.306G>A	p.Met102Ile	missense_variant	8/21		NM_001349338.3	ENSP00000497369	P4	Q9H334-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000398

AC:

AN:

251370

Hom.:

AF XY:

0.00000736

AC XY:

AN XY:

135852

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000880

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000274

AC:

AN:

1461808

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

727210

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:

0.0000187

Gnomad4 NFE exome

AF:

8.99e-7

Gnomad4 OTH exome

AF:

0.0000331

GnomAD4 genome

Cov.:

Alfa

AF:

0.0000312

Hom.:

Bravo

AF:

0.00000378

ExAC

AF:

0.00000824

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Feb 08, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.78

BayesDel_addAF

Pathogenic

0.34

BayesDel_noAF

Pathogenic

0.25

CADD

Pathogenic

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.72

D;.;D;.;D;.;.;.;.;.;.;.;D;.;.;.;D;.;.;D;.;.;.;.;.;.;.;T;.

Eigen

Uncertain

0.54

Eigen_PC

Uncertain

0.62

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.96

.;D;.;.;.;.;D;.;.;D;D;D;.;.;D;.;.;D;D;D;D;D;D;D;D;D;D;D;.

M_CAP

Uncertain

0.10

MetaRNN

Uncertain

0.46

T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T

MetaSVM

Uncertain

0.63

MutationAssessor

Uncertain

2.6

M;M;M;M;M;.;.;.;M;.;.;.;M;.;.;.;M;M;.;M;.;.;.;.;.;.;.;.;.

MutationTaster

Benign

1.0

D;D;D;D;D;D;D

PrimateAI

Pathogenic

0.85

PROVEAN

Uncertain

-2.6

D;.;D;D;.;.;.;.;.;.;.;.;D;.;.;N;.;.;.;.;.;D;.;.;D;.;D;.;.

REVEL

Benign

0.29

Sift

Benign

0.071

T;.;T;T;.;.;.;.;.;.;.;.;T;.;.;T;.;.;.;.;.;T;.;.;T;.;D;.;.

Sift4G

Benign

0.14

T;T;T;T;.;.;.;T;.;.;.;.;T;.;.;T;.;.;.;.;.;T;.;.;.;.;T;.;.

Polyphen

0.53

P;.;P;.;P;.;.;.;.;.;.;.;P;.;.;.;P;.;.;P;.;.;.;.;.;.;.;.;.

Vest4

0.74

MutPred

0.18

Gain of catalytic residue at P104 (P = 0.0327);Gain of catalytic residue at P104 (P = 0.0327);Gain of catalytic residue at P104 (P = 0.0327);Gain of catalytic residue at P104 (P = 0.0327);Gain of catalytic residue at P104 (P = 0.0327);Gain of catalytic residue at P104 (P = 0.0327);.;.;Gain of catalytic residue at P104 (P = 0.0327);Gain of catalytic residue at P104 (P = 0.0327);.;.;Gain of catalytic residue at P104 (P = 0.0327);.;Gain of catalytic residue at P104 (P = 0.0327);.;Gain of catalytic residue at P104 (P = 0.0327);Gain of catalytic residue at P104 (P = 0.0327);.;Gain of catalytic residue at P104 (P = 0.0327);.;Gain of catalytic residue at P104 (P = 0.0327);.;Gain of catalytic residue at P104 (P = 0.0327);.;.;.;Gain of catalytic residue at P104 (P = 0.0327);Gain of catalytic residue at P104 (P = 0.0327);

MVP

0.80

MPC

0.78

ClinPred

0.65

GERP RS

5.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.42

gMVP

0.23

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.16

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over