19-54110114-T-A

Variant names:

• chr19-54110114-T-A
• NM_013342.4:c.290A>T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_013342.4(TFPT):​c.290A>T​(p.Glu97Val) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: TFPT NM_013342.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.64

Genes affected

TFPT (HGNC:13630): (TCF3 fusion partner) Predicted to enable DNA binding activity and protein kinase binding activity. Involved in apoptotic signaling pathway. Located in nucleoplasm. Part of Ino80 complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.757

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TFPT	NM_013342.4	c.290A>T	p.Glu97Val	missense_variant	Exon 3 of 6	ENST00000391759.6	NP_037474.1
TFPT	NM_001321792.2	c.263A>T	p.Glu88Val	missense_variant	Exon 3 of 6		NP_001308721.1
TFPT	XM_005278261.2	c.-71A>T		5_prime_UTR_variant	Exon 2 of 5		XP_005278318.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TFPT	ENST00000391759.6	c.290A>T	p.Glu97Val	missense_variant	Exon 3 of 6	1	NM_013342.4	ENSP00000375639.1
TFPT	ENST00000391758.5	c.263A>T	p.Glu88Val	missense_variant	Exon 3 of 6	1		ENSP00000375638.1
TFPT	ENST00000391757.1	c.290A>T	p.Glu97Val	missense_variant	Exon 3 of 6	5		ENSP00000375637.1
TFPT	ENST00000420715.6	n.283-1719A>T		intron_variant	Intron 2 of 4	5		ENSP00000395180.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jul 19, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.290A>T (p.E97V) alteration is located in exon 3 (coding exon 3) of the TFPT gene. This alteration results from a A to T substitution at nucleotide position 290, causing the glutamic acid (E) at amino acid position 97 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.92
BayesDel_addAF	Pathogenic	0.40	D
BayesDel_noAF	Pathogenic	0.34
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.65	D;.;.
Eigen	Uncertain	0.34
Eigen_PC	Uncertain	0.36
FATHMM_MKL	Uncertain	0.90	D
LIST_S2	Benign	0.84	.;T;D
M_CAP	Benign	0.027	D
MetaRNN	Pathogenic	0.76	D;D;D
MetaSVM	Benign	-0.60	T
MutationAssessor	Uncertain	2.0	M;.;.
PrimateAI	Pathogenic	0.87	D
PROVEAN	Pathogenic	-5.6	D;D;D
REVEL	Uncertain	0.38
Sift	Uncertain	0.0010	D;D;D
Sift4G	Uncertain	0.0030	D;D;D
Polyphen		0.74	P;.;.
Vest4		0.90
MutPred		0.24		Loss of disorder (P = 0.2312);.;Loss of disorder (P = 0.2312);
MVP		0.47
MPC		0.24
ClinPred		0.98	D
GERP RS		4.5
Varity_R		0.57
gMVP		0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-54613497;