chr14-28767055-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_005249.5(FOXG1):​c.-210del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0123 in 143,078 control chromosomes in the GnomAD database, including 18 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.011 ( 18 hom., cov: 29)
Exomes 𝑓: 0.068 ( 0 hom. )

Consequence

FOXG1
NM_005249.5 5_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0490
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)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 14-28767055-CT-C is Benign according to our data. Variant chr14-28767055-CT-C is described in ClinVar as [Likely_benign]. Clinvar id is 1188300.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0935 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FOXG1NM_005249.5 linkuse as main transcriptc.-210del 5_prime_UTR_variant 1/1 ENST00000313071.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FOXG1ENST00000313071.7 linkuse as main transcriptc.-210del 5_prime_UTR_variant 1/1 NM_005249.5 P1
FOXG1ENST00000706482.1 linkuse as main transcriptc.-210del 5_prime_UTR_variant 2/2 P1
LINC01551ENST00000675861.1 linkuse as main transcriptn.374+1057del intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0109
AC:
1524
AN:
139646
Hom.:
18
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.0338
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00626
Gnomad ASJ
AF:
0.000304
Gnomad EAS
AF:
0.00165
Gnomad SAS
AF:
0.000905
Gnomad FIN
AF:
0.000130
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00172
Gnomad OTH
AF:
0.0105
GnomAD4 exome
AF:
0.0685
AC:
235
AN:
3432
Hom.:
0
Cov.:
0
AF XY:
0.0759
AC XY:
149
AN XY:
1962
show subpopulations
Gnomad4 AFR exome
AF:
0.0400
Gnomad4 AMR exome
AF:
0.200
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0357
Gnomad4 SAS exome
AF:
0.119
Gnomad4 FIN exome
AF:
0.0459
Gnomad4 NFE exome
AF:
0.0626
Gnomad4 OTH exome
AF:
0.0385
GnomAD4 genome
AF:
0.0109
AC:
1522
AN:
139646
Hom.:
18
Cov.:
29
AF XY:
0.0107
AC XY:
726
AN XY:
67582
show subpopulations
Gnomad4 AFR
AF:
0.0337
Gnomad4 AMR
AF:
0.00625
Gnomad4 ASJ
AF:
0.000304
Gnomad4 EAS
AF:
0.00165
Gnomad4 SAS
AF:
0.000911
Gnomad4 FIN
AF:
0.000130
Gnomad4 NFE
AF:
0.00170
Gnomad4 OTH
AF:
0.0105

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxAug 21, 2019- -

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