18-3447339-TA-T

Variant names:

• chr18-3447339-TA-T
• rs11421150
• NM_001278686.3:c.-44-9000delA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_174886.3(TGIF1):​c.-44-9000delA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.023 (86 hom., cov: 0)
• Consequence: TGIF1 NM_174886.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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 Benign. Variant got -10 ACMG points.

• BP6: Variant 18-3447339-TA-T is Benign according to our data. Variant chr18-3447339-TA-T is described in ClinVar as [Benign]. Clinvar id is 1282084.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0631 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0225 AC: 3185 AN: 141544 Hom.: 86 Cov.: 0

Gnomad AFR AF: 0.0653

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0110

Gnomad ASJ AF: 0.00594

Gnomad EAS AF: 0.0299

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.00849

Gnomad MID AF: 0.00968

Gnomad NFE AF: 0.00256

Gnomad OTH AF: 0.0190

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

GnomAD4 genome AF: 0.0225 AC: 3190 AN: 141580 Hom.: 86 Cov.: 0 AF XY: 0.0222 AC XY: 1516 AN XY: 68250

Gnomad4 AFR AF: 0.0652

Gnomad4 AMR AF: 0.0109

Gnomad4 ASJ AF: 0.00594

Gnomad4 EAS AF: 0.0302

Gnomad4 SAS AF: 0.0171

Gnomad4 FIN AF: 0.00849

Gnomad4 NFE AF: 0.00256

Gnomad4 OTH AF: 0.0194

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 20, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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;