NM_001143975.1:c.187A>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001143975.1(UBTFL1):​c.187A>T​(p.Ile63Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 27)

Consequence

UBTFL1
NM_001143975.1 missense

Scores

5
6

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.48
Variant links:
Genes affected
UBTFL1 (HGNC:14533): (upstream binding transcription factor like 1) Predicted to enable DNA binding activity. Predicted to act upstream of or within blastocyst growth; embryo implantation; and regulation of gene expression. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2541595).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
UBTFL1NM_001143975.1 linkc.187A>T p.Ile63Phe missense_variant Exon 1 of 1 ENST00000530464.2 NP_001137447.1 P0CB47

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
UBTFL1ENST00000530464.2 linkc.187A>T p.Ile63Phe missense_variant Exon 1 of 1 6 NM_001143975.1 ENSP00000485108.1 P0CB47

Frequencies

GnomAD3 genomes
Cov.:
27
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
27

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Oct 01, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.187A>T (p.I63F) alteration is located in exon 1 (coding exon 1) of the UBTFL1 gene. This alteration results from a A to T substitution at nucleotide position 187, causing the isoleucine (I) at amino acid position 63 to be replaced by a phenylalanine (F). 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
Benign
0.24
BayesDel_addAF
Uncertain
0.061
T
BayesDel_noAF
Benign
-0.15
CADD
Benign
20
DANN
Benign
0.78
DEOGEN2
Benign
0.15
T
FATHMM_MKL
Benign
0.62
D
LIST_S2
Uncertain
0.90
D
MetaRNN
Benign
0.25
T
MutationAssessor
Uncertain
2.3
M
PrimateAI
Uncertain
0.67
T
Sift4G
Uncertain
0.020
D
Polyphen
1.0
D
Vest4
0.20
MVP
0.014
GERP RS
-0.17
Varity_R
0.061
gMVP
0.33

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: chr11-89819304; API