rs11421150

Variant names:

• chr18-3447339-TAAAA-T
• rs11421150
• NM_001278686.3:c.-44-9003_-44-9000delAAAA

Your query was ambiguous. Multiple possible variants found:

• chr18-3447339-TAAAA-T
• chr18-3447339-TAAAA-TA
• chr18-3447339-TAAAA-TAA
• chr18-3447339-TAAAA-TAAA
• chr18-3447339-TAAAA-TAAAAA
• chr18-3447339-TAAAA-TAAAAAA
• chr18-3447339-TAAAA-TAAAAAAA
• chr18-3447339-TAAAA-TAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_174886.3(TGIF1):​c.-44-9003_-44-9000delAAAA 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: not found (cov: 0)
• Consequence: TGIF1 NM_174886.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266

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]

LOC124904237 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TGIF1	NM_001278686.3	c.-44-9003_-44-9000delAAAA		intron_variant	Intron 2 of 3		NP_001265615.1
TGIF1	NM_174886.3	c.-44-9003_-44-9000delAAAA		intron_variant	Intron 2 of 3		NP_777480.1
LOC124904237	XR_007066269.1	n.126-157_126-154delTTTT		intron_variant	Intron 1 of 1
TGIF1	NM_173207.4	c.-400_-397delAAAA		upstream_gene_variant			NP_775299.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TGIF1	ENST00000401449.5	c.-44-9014_-44-9011delAAAA		intron_variant	Intron 2 of 3	2		ENSP00000385206.1
TGIF1	ENST00000548489.6	c.-44-9014_-44-9011delAAAA		intron_variant	Intron 2 of 3	3		ENSP00000447747.2
TGIF1	ENST00000552383.5	c.-44-9014_-44-9011delAAAA		intron_variant	Intron 2 of 3	2		ENSP00000449287.1
TGIF1	ENST00000550958.5	c.-44-9014_-44-9011delAAAA		intron_variant	Intron 2 of 3	3		ENSP00000449531.1

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11421150; hg19: chr18-3447337;