1-20190986-T-C

Variant names:

• chr1-20190986-T-C
• NM_152376.5:c.425T>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_152376.5(UBXN10):​c.425T>C​(p.Leu142Pro) 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. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: UBXN10 NM_152376.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.887
• Publications: 0 publications found

Genes affected

UBXN10 (HGNC:26354): (UBX domain protein 10) Involved in cilium assembly. Located in cilium. Colocalizes with intraciliary transport particle B. [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=0.09079796).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152376.5. 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
	UBXN10	NM_152376.5	MANE Select	c.425T>C	p.Leu142Pro	missense	Exon 2 of 2	NP_689589.1	Q96LJ8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBXN10	ENST00000375099.4	TSL:1 MANE Select	c.425T>C	p.Leu142Pro	missense	Exon 2 of 2	ENSP00000364240.3	Q96LJ8
	UBXN10	ENST00000866634.1		c.425T>C	p.Leu142Pro	missense	Exon 2 of 2	ENSP00000536693.1
	UBXN10	ENST00000866635.1		c.425T>C	p.Leu142Pro	missense	Exon 2 of 2	ENSP00000536694.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

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	0.11
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	15
DANN	Uncertain	0.99
DEOGEN2	Benign	0.090	T
Eigen	Benign	-0.46
Eigen_PC	Benign	-0.43
FATHMM_MKL	Benign	0.33	N
LIST_S2	Benign	0.40	T
M_CAP	Benign	0.0072	T
MetaRNN	Benign	0.091	T
MetaSVM	Benign	-0.83	T
MutationAssessor	Benign	1.8	L
PhyloP100		0.89
PrimateAI	Benign	0.31	T
PROVEAN	Uncertain	-2.9	D
REVEL	Benign	0.037
Sift	Benign	0.049	D
Sift4G	Benign	0.15	T
Polyphen		0.053	B
Vest4		0.12
MutPred		0.53		Gain of relative solvent accessibility (P = 0.0479)
MVP		0.099
MPC		0.24
ClinPred		0.34	T
GERP RS		2.7
Varity_R		0.32
gMVP		0.60
Mutation Taster		=63/37	polymorphism

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: chr1-20517479;