11-90086324-G-A

Variant names:

• chr11-90086324-G-A
• rs1951025669
• NM_001143975.1:c.375G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001143975.1(UBTFL1):​c.375G>A​(p.Met125Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 9/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 24)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: UBTFL1 NM_001143975.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.55
• 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: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.17038283).

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.375G>A	p.Met125Ile	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.375G>A	p.Met125Ile	missense	Exon 1 of 1	ENSP00000485108.1	P0CB47

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 139166 Hom.: 0 Cov.: 24

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1369922 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 682458

African (AFR) AF: 0.00 AC: 0 AN: 32320

American (AMR) AF: 0.00 AC: 0 AN: 31158

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25464

East Asian (EAS) AF: 0.00 AC: 0 AN: 34610

South Asian (SAS) AF: 0.00 AC: 0 AN: 81120

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47792

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5518

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1054556

Other (OTH) AF: 0.00 AC: 0 AN: 57384

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 139166 Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0 AN XY: 67158

African (AFR) AF: 0.00 AC: 0 AN: 38940

American (AMR) AF: 0.00 AC: 0 AN: 12176

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3382

East Asian (EAS) AF: 0.00 AC: 0 AN: 4252

South Asian (SAS) AF: 0.00 AC: 0 AN: 4292

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8758

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 298

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 64330

Other (OTH) AF: 0.00 AC: 0 AN: 1880

Alfa AF: 0.00 Hom.: 0

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	0.34
BayesDel_addAF	Benign	-0.00016	T
BayesDel_noAF	Benign	-0.24
CADD	Benign	5.8
DANN	Benign	0.53
DEOGEN2	Uncertain	0.54	D
FATHMM_MKL	Benign	0.50	N
LIST_S2	Benign	0.35	T
MetaRNN	Benign	0.17	T
MutationAssessor	Benign	0.67	N
PhyloP100		3.5
PrimateAI	Uncertain	0.54	T
Sift4G	Benign	0.12	T
Polyphen		0.0050	B
Vest4		0.20
MVP		0.055
GERP RS		0.084
PromoterAI		0.0012	Neutral
Varity_R		0.41
gMVP		0.21

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

dbSNP: rs1951025669; hg19: chr11-89819492;