19-54114448-G-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7

The NM_013342.4(TFPT):​c.276C>A​(p.Ile92Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,418 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

TFPT
NM_013342.4 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.247
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP7
Synonymous conserved (PhyloP=0.247 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TFPTNM_013342.4 linkc.276C>A p.Ile92Ile synonymous_variant Exon 2 of 6 ENST00000391759.6 NP_037474.1 P0C1Z6-1A0A024R4Q5
TFPTNM_001321792.2 linkc.249C>A p.Ile83Ile synonymous_variant Exon 2 of 6 NP_001308721.1 P0C1Z6-2
TFPTXM_005278261.2 linkc.-89C>A 5_prime_UTR_variant Exon 1 of 5 XP_005278318.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TFPTENST00000391759.6 linkc.276C>A p.Ile92Ile synonymous_variant Exon 2 of 6 1 NM_013342.4 ENSP00000375639.1 P0C1Z6-1
TFPTENST00000391758.5 linkc.249C>A p.Ile83Ile synonymous_variant Exon 2 of 6 1 ENSP00000375638.1 P0C1Z6-2
TFPTENST00000391757.1 linkc.276C>A p.Ile92Ile synonymous_variant Exon 2 of 6 5 ENSP00000375637.1 A8MTQ3
TFPTENST00000420715.6 linkn.276C>A non_coding_transcript_exon_variant Exon 2 of 5 5 ENSP00000395180.1 F8WDC1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.85e-7
AC:
1
AN:
1460418
Hom.:
0
Cov.:
32
AF XY:
0.00000138
AC XY:
1
AN XY:
726366
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.00e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.41
CADD
Benign
11
DANN
Benign
0.93

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-54617828; API