Genetic Variant UBXN10:p.His35_Ser41dup (chr1-20190663-G-GCACATGATAAGGCCCAAGTCC) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBS1BS2

The NM_152376.5(UBXN10):c.103_123dupCACATGATAAGGCCCAAGTCC(p.His35_Ser41dup) variant causes a conservative inframe insertion change. The variant allele was found at a frequency of 0.00071 in 1,614,180 control chromosomes in the GnomAD database, including 15 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00081 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00070 ( 15 hom. )

Consequence

UBXN10
NM_152376.5 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.99

Variant links:

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]

UBXN10 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_152376.5.

BP6

Variant 1-20190663-G-GCACATGATAAGGCCCAAGTCC is Benign according to our data. Variant chr1-20190663-G-GCACATGATAAGGCCCAAGTCC is described in ClinVar as [Benign]. Clinvar id is 1265956.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000814 (124/152286) while in subpopulation EAS AF= 0.0186 (96/5170). AF 95% confidence interval is 0.0156. There are 0 homozygotes in gnomad4. There are 67 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAdExome4 at 15 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBXN10	NM_152376.5 link	c.103_123dupCACATGATAAGGCCCAAGTCC	p.His35_Ser41dup	conservative_inframe_insertion	Exon 2 of 2	ENST00000375099.4	NP_689589.1	Q96LJ8
UBXN10	XM_005245742.5 link	c.103_123dupCACATGATAAGGCCCAAGTCC	p.His35_Ser41dup	conservative_inframe_insertion	Exon 2 of 2		XP_005245799.1	Q96LJ8
UBXN10	XM_011540699.4 link	c.103_123dupCACATGATAAGGCCCAAGTCC	p.His35_Ser41dup	conservative_inframe_insertion	Exon 2 of 2		XP_011539001.1	Q96LJ8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBXN10	ENST00000375099.4 link	c.103_123dupCACATGATAAGGCCCAAGTCC	p.His35_Ser41dup	conservative_inframe_insertion	Exon 2 of 2	1	NM_152376.5	ENSP00000364240.3		Q96LJ8

Frequencies

GnomAD3 genomes

AF:

0.000815

AC:

124

AN:

152168

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000589

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0185

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000162

Gnomad OTH

AF:

0.000479

GnomAD3 exomes

AF:

0.00139

AC:

348

AN:

250486

Hom.:

AF XY:

0.00140

AC XY:

190

AN XY:

135504

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0165

Gnomad SAS exome

AF:

0.00101

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000532

Gnomad OTH exome

AF:

0.00130

GnomAD4 exome

AF:

0.000699

AC:

1022

AN:

1461894

Hom.:

Cov.:

AF XY:

0.000718

AC XY:

522

AN XY:

727248

show subpopulations

Gnomad4 AFR exome

AF:

0.0000299

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0198

Gnomad4 SAS exome

AF:

0.00104

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000620

Gnomad4 OTH exome

AF:

0.00126

GnomAD4 genome

AF:

0.000814

AC:

124

AN:

152286

Hom.:

Cov.:

AF XY:

0.000900

AC XY:

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.0000241

Gnomad4 AMR

AF:

0.000588

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0186

Gnomad4 SAS

AF:

0.00124

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000162

Gnomad4 OTH

AF:

0.000474

Alfa

AF:

0.000257

Hom.:

Asia WGS

AF:

0.00837

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

May 08, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

In-frame duplication of 7 amino acids in a non-repeat region; Has not been previously published as pathogenic or benign to our knowledge; Variants in candidate genes are classified as variants of uncertain significance in accordance with ACMG guidelines (Richards et al., 2015) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over