chr1-20191103-A-T

Variant names:

• chr1-20191103-A-T
• NM_152376.5:c.542A>T

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.542A>T​(p.Gln181Leu) 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: 0.150
• 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=0.09095073).

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.542A>T	p.Gln181Leu	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.542A>T	p.Gln181Leu	missense	Exon 2 of 2	ENSP00000364240.3	Q96LJ8
	UBXN10	ENST00000866634.1		c.542A>T	p.Gln181Leu	missense	Exon 2 of 2	ENSP00000536693.1
	UBXN10	ENST00000866635.1		c.542A>T	p.Gln181Leu	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	0.10
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.41
CADD	Benign	17
DANN	Benign	0.94
DEOGEN2	Benign	0.28	T
Eigen	Benign	-0.79
Eigen_PC	Benign	-0.87
FATHMM_MKL	Benign	0.083	N
LIST_S2	Benign	0.40	T
M_CAP	Benign	0.0083	T
MetaRNN	Benign	0.091	T
MetaSVM	Benign	-0.97	T
MutationAssessor	Uncertain	2.1	M
PhyloP100		0.15
PrimateAI	Benign	0.29	T
PROVEAN	Pathogenic	-4.6	D
REVEL	Benign	0.057
Sift	Uncertain	0.013	D
Sift4G	Uncertain	0.0080	D
Polyphen		0.028	B
Vest4		0.15
MutPred		0.44		Loss of methylation at K179 (P = 0.0534)
MVP		0.040
MPC		0.38
ClinPred		0.28	T
GERP RS		0.92
Varity_R		0.18
gMVP		0.60
Mutation Taster		=89/11	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: chr1-20517596;