14-28767055-CTTTTTTT-CTTTTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_005249.5(FOXG1):​c.-211_-210delTT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000245 in 143,100 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00012 ( 0 hom., cov: 29)
Exomes 𝑓: 0.0053 ( 0 hom. )

Consequence

FOXG1
NM_005249.5 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.233
Variant links:
Genes affected
FOXG1 (HGNC:3811): (forkhead box G1) This locus encodes a member of the fork-head transcription factor family. The encoded protein, which functions as a transcriptional repressor, is highly expressed in neural tissues during brain development. Mutations at this locus have been associated with Rett syndrome and a diverse spectrum of neurodevelopmental disorders defined as part of the FOXG1 syndrome. This gene is disregulated in many types of cancer and is the target of multiple microRNAs that regulate the proliferation of tumor cells. [provided by RefSeq, Jul 2020]
LINC01551 (HGNC:19828): (long intergenic non-protein coding RNA 1551)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1
Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.00526 (18/3420) while in subpopulation EAS AF= 0.0357 (1/28). AF 95% confidence interval is 0.00423. There are 0 homozygotes in gnomad4_exome. There are 11 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
BS2
High AC in GnomAd4 at 17 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FOXG1NM_005249.5 linkc.-211_-210delTT 5_prime_UTR_variant Exon 1 of 1 ENST00000313071.7 NP_005240.3 P55316

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FOXG1ENST00000313071 linkc.-211_-210delTT 5_prime_UTR_variant Exon 1 of 1 NM_005249.5 ENSP00000339004.3 P55316
FOXG1ENST00000706482 linkc.-211_-210delTT 5_prime_UTR_variant Exon 2 of 2 ENSP00000516406.1 P55316
LINC01551ENST00000675861.1 linkn.374+1056_374+1057delTT intron_variant Intron 1 of 3

Frequencies

GnomAD3 genomes
AF:
0.000122
AC:
17
AN:
139680
Hom.:
0
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.000418
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000711
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
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:
0.00526
AC:
18
AN:
3420
Hom.:
0
AF XY:
0.00561
AC XY:
11
AN XY:
1962
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0357
Gnomad4 SAS exome
AF:
0.0107
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00478
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.000122
AC:
17
AN:
139680
Hom.:
0
Cov.:
29
AF XY:
0.000148
AC XY:
10
AN XY:
67590
show subpopulations
Gnomad4 AFR
AF:
0.000418
Gnomad4 AMR
AF:
0.0000711
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

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.

Other links and lift over

dbSNP: rs542787885; hg19: chr14-29236261; API