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

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2

The NM_004473.4(FOXE1):c.520_537del(p.Ala174_Ala179del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.000244 in 1,220,050 control chromosomes in the GnomAD database, including 4 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00034 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00023 ( 4 hom. )

Consequence

FOXE1
NM_004473.4 inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.03

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 -5 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_004473.4

BS2

High Homozygotes in GnomAdExome4 at 4 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOXE1	NM_004473.4 linkuse as main transcript	c.520_537del	p.Ala174_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.520_537del	p.Ala174_Ala179del	inframe_deletion	1/1		NM_004473.4	P1

Frequencies

GnomAD3 genomes

AF:

0.000331

AC:

AN:

144856

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000399

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00116

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000626

Gnomad SAS

AF:

0.000849

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000123

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000232

AC:

249

AN:

1075094

Hom.:

AF XY:

0.000270

AC XY:

140

AN XY:

518060

show subpopulations

Gnomad4 AFR exome

AF:

0.000327

Gnomad4 AMR exome

AF:

0.000889

Gnomad4 ASJ exome

AF:

0.000475

Gnomad4 EAS exome

AF:

0.000252

Gnomad4 SAS exome

AF:

0.000910

Gnomad4 FIN exome

AF:

0.0000793

Gnomad4 NFE exome

AF:

0.000187

Gnomad4 OTH exome

AF:

0.000553

GnomAD4 genome

AF:

0.000338

AC:

AN:

144956

Hom.:

Cov.:

AF XY:

0.000411

AC XY:

AN XY:

70600

show subpopulations

Gnomad4 AFR

AF:

0.000398

Gnomad4 AMR

AF:

0.00116

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000837

Gnomad4 SAS

AF:

0.000850

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000123

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.

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