11-90086136-A-T

Variant names:

• chr11-90086136-A-T
• NM_001143975.1:c.187A>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_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
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.48
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001143975.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBTFL1	NM_001143975.1	MANE Select	c.187A>T	p.Ile63Phe	missense	Exon 1 of 1	NP_001137447.1	P0CB47

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBTFL1	ENST00000530464.2	TSL:6 MANE Select	c.187A>T	p.Ile63Phe	missense	Exon 1 of 1	ENSP00000485108.1	P0CB47

Frequencies

GnomAD3 genomes Cov.: 27

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 27

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

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
PhyloP100		2.5
PrimateAI	Uncertain	0.67	T
Sift4G	Uncertain	0.020	D
Polyphen		1.0	D
Vest4		0.20
MVP		0.014
GERP RS		-0.17
PromoterAI		-0.0044	Neutral
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

Other links and lift over

hg19: chr11-89819304;