Variant 9-97854418-AGCCGCCGCCGCCGCCGCCGCCGCC-AGCCGCCGCCGCCGCCGCCGCC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP3BP6

The NM_004473.4(FOXE1):c.535_537del(p.Ala179del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000357 in 1,218,460 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.00019 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00038 ( 0 hom. )

Consequence

FOXE1
NM_004473.4 inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.56

Variant links:

Genes affected

FOXE1 (HGNC:3806): (forkhead box E1) This intronless gene encodes a protein that belongs to the forkhead family of transcription factors. Members of this family contain a conserved 100-amino acid DNA-binding 'forkhead' domain. The encoded protein functions as a thyroid transcription factor that plays a role in thyroid morphogenesis. Mutations in this gene are associated with the Bamforth-Lazarus syndrome, and with susceptibility to nonmedullary thyroid cancer-4. [provided by RefSeq, Nov 2016]

FOXE1 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_004473.4

BP6

Variant 9-97854418-AGCC-A is Benign according to our data. Variant chr9-97854418-AGCC-A is described in Lovd as [Benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOXE1	NM_004473.4 linkuse as main transcript	c.535_537del	p.Ala179del	inframe_deletion	1/1	ENST00000375123.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOXE1	ENST00000375123.5 linkuse as main transcript	c.535_537del	p.Ala179del	inframe_deletion	1/1		NM_004473.4	P1

Frequencies

GnomAD3 genomes

AF:

0.000193

AC:

AN:

144846

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000200

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000273

Gnomad ASJ

AF:

0.000888

Gnomad EAS

AF:

0.000834

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000123

Gnomad OTH

AF:

0.000498

GnomAD4 exome

AF:

0.000379

AC:

407

AN:

1073514

Hom.:

AF XY:

0.000433

AC XY:

224

AN XY:

517220

show subpopulations

Gnomad4 AFR exome

AF:

0.000327

Gnomad4 AMR exome

AF:

0.00153

Gnomad4 ASJ exome

AF:

0.000555

Gnomad4 EAS exome

AF:

0.000587

Gnomad4 SAS exome

AF:

0.000753

Gnomad4 FIN exome

AF:

0.000557

Gnomad4 NFE exome

AF:

0.000340

Gnomad4 OTH exome

AF:

0.000530

GnomAD4 genome

AF:

0.000193

AC:

AN:

144946

Hom.:

Cov.:

AF XY:

0.000156

AC XY:

AN XY:

70594

show subpopulations

Gnomad4 AFR

AF:

0.000199

Gnomad4 AMR

AF:

0.000273

Gnomad4 ASJ

AF:

0.000888

Gnomad4 EAS

AF:

0.000837

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000123

Gnomad4 OTH

AF:

0.000493

ClinVar

Not reported in ClinVar

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over