Genetic Variant TGIF1:c.-44-9001_-44-9000dupAA (chr18-3447339-T-TAA) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_174886.3(TGIF1):c.-44-9001_-44-9000dupAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0053 ( 5 hom., cov: 0)

Consequence

TGIF1
NM_174886.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.266

Publications

0 publications found

Variant links:

Genes affected

TGIF1 (HGNC:11776): (TGFB induced factor homeobox 1) The protein encoded by this gene is a member of the three-amino acid loop extension (TALE) superclass of atypical homeodomains. TALE homeobox proteins are highly conserved transcription regulators. This particular homeodomain binds to a previously characterized retinoid X receptor responsive element from the cellular retinol-binding protein II promoter. In addition to its role in inhibiting 9-cis-retinoic acid-dependent RXR alpha transcription activation of the retinoic acid responsive element, the protein is an active transcriptional co-repressor of SMAD2 and may participate in the transmission of nuclear signals during development and in the adult. Mutations in this gene are associated with holoprosencephaly type 4, which is a structural anomaly of the brain. Alternative splicing has been observed at this locus and multiple splice variants encoding distinct isoforms are described. [provided by RefSeq, Jul 2013]

TGIF1 Gene-Disease associations (from GenCC):

holoprosencephaly 4
Inheritance: AD Classification: DEFINITIVE, STRONG, LIMITED Submitted by: PanelApp Australia, Laboratory for Molecular Medicine, G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)

TGIF1 links:

ENSG00000302876 (HGNC:):

ENSG00000302876 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High AC in GnomAd4 at 754 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_174886.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein	UniProt
TGIF1	NM_001278686.3	c.-44-9001_-44-9000dupAA	intron	N/A	NP_001265615.1	Q15583-4
TGIF1	NM_174886.3	c.-44-9001_-44-9000dupAA	intron	N/A	NP_777480.1	Q15583-4
TGIF1	NM_173207.4	c.-401_-400insAA	upstream_gene	N/A	NP_775299.1	Q15583-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TGIF1	ENST00000401449.5	TSL:2	c.-44-9015_-44-9014insAA	intron	N/A	ENSP00000385206.1	Q15583-4
TGIF1	ENST00000548489.6	TSL:3	c.-44-9015_-44-9014insAA	intron	N/A	ENSP00000447747.2	Q15583-4
TGIF1	ENST00000552383.5	TSL:2	c.-44-9015_-44-9014insAA	intron	N/A	ENSP00000449287.1	F8VWK5

Frequencies

GnomAD3 genomes

AF:

0.00532

AC:

754

AN:

141652

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0148

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00213

Gnomad ASJ

AF:

0.00148

Gnomad EAS

AF:

0.000203

Gnomad SAS

AF:

0.00318

Gnomad FIN

AF:

0.000996

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00178

Gnomad OTH

AF:

0.00462

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.00532

AC:

754

AN:

141688

Hom.:

Cov.:

AF XY:

0.00543

AC XY:

371

AN XY:

68322

show subpopulations

African (AFR)

AF:

0.0148

AC:

571

AN:

38592

American (AMR)

AF:

0.00213

AC:

AN:

14094

Ashkenazi Jewish (ASJ)

AF:

0.00148

AC:

AN:

3368

East Asian (EAS)

AF:

0.000204

AC:

AN:

4902

South Asian (SAS)

AF:

0.00319

AC:

AN:

4388

European-Finnish (FIN)

AF:

0.000996

AC:

AN:

8034

Middle Eastern (MID)

AF:

0.00

AC:

AN:

284

European-Non Finnish (NFE)

AF:

0.00178

AC:

116

AN:

65188

Other (OTH)

AF:

0.00458

AC:

AN:

1964

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

107

142

178

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00286

Hom.:

416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.27

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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18-3447339-TAAAA-TAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over