Variant chr3-70955638-T-TA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_001349338.3(FOXP1):c.*3608_*3609insT variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.00389 in 233,496 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0036 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0045 ( 1 hom. )

Consequence

FOXP1
NM_001349338.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.31

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 3-70955638-T-TA is Benign according to our data. Variant chr3-70955638-T-TA is described in ClinVar as [Likely_benign]. Clinvar id is 346556.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00358 (545/152194) while in subpopulation SAS AF= 0.0147 (71/4818). AF 95% confidence interval is 0.012. There are 4 homozygotes in gnomad4. There are 276 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 545 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOXP1	NM_001349338.3 linkuse as main transcript	c.3608_3609insT		3_prime_UTR_variant	21/21	ENST00000649528.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOXP1	ENST00000649528.3 linkuse as main transcript	c.3608_3609insT		3_prime_UTR_variant	21/21		NM_001349338.3	P4	Q9H334-1
FOXP1	ENST00000318789.11 linkuse as main transcript	c.3608_3609insT		3_prime_UTR_variant	21/21	1		P4	Q9H334-1

Frequencies

GnomAD3 genomes

AF:

0.00359

AC:

546

AN:

152076

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000725

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000787

Gnomad ASJ

AF:

0.0115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0147

Gnomad FIN

AF:

0.00302

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00515

Gnomad OTH

AF:

0.00431

GnomAD4 exome

AF:

0.00448

AC:

364

AN:

81302

Hom.:

Cov.:

AF XY:

0.00489

AC XY:

183

AN XY:

37416

show subpopulations

Gnomad4 AFR exome

AF:

0.000257

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00898

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0214

Gnomad4 FIN exome

AF:

0.00881

Gnomad4 NFE exome

AF:

0.00522

Gnomad4 OTH exome

AF:

0.00473

GnomAD4 genome

AF:

0.00358

AC:

545

AN:

152194

Hom.:

Cov.:

AF XY:

0.00371

AC XY:

276

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.000723

Gnomad4 AMR

AF:

0.000786

Gnomad4 ASJ

AF:

0.0115

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0147

Gnomad4 FIN

AF:

0.00302

Gnomad4 NFE

AF:

0.00515

Gnomad4 OTH

AF:

0.00380

Alfa

AF:

0.00432

Hom.:

Bravo

AF:

0.00297

Asia WGS

AF:

0.00722

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Intellectual Disability with Language Impairment and Autistic Features

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 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.

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