Variant chrX-154485912-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_014235.5(UBL4A):c.222G>A(p.Leu74=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00605 in 1,209,497 control chromosomes in the GnomAD database, including 25 homozygotes. There are 2,320 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. L74L) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0044 ( 3 hom., 152 hem., cov: 24)

Exomes 𝑓: 0.0062 ( 22 hom. 2168 hem. )

Consequence

UBL4A
NM_014235.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.254

Variant links:

Genes affected

UBL4A (HGNC:12505): (ubiquitin like 4A) Enables chaperone binding activity. Involved in tail-anchored membrane protein insertion into ER membrane. Located in cytosol; membrane; and nucleoplasm. Part of BAT3 complex. [provided by Alliance of Genome Resources, Apr 2022]

UBL4A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP6

Variant X-154485912-C-T is Benign according to our data. Variant chrX-154485912-C-T is described in ClinVar as [Benign]. Clinvar id is 771063.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.254 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBL4A	NM_014235.5 linkuse as main transcript	c.222G>A	p.Leu74=	synonymous_variant	3/4	ENST00000369660.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBL4A	ENST00000369660.9 linkuse as main transcript	c.222G>A	p.Leu74=	synonymous_variant	3/4	1	NM_014235.5	P1

Frequencies

GnomAD3 genomes

AF:

0.00441

AC:

496

AN:

112391

Hom.:

Cov.:

AF XY:

0.00440

AC XY:

152

AN XY:

34545

show subpopulations

Gnomad AFR

AF:

0.000808

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00316

Gnomad ASJ

AF:

0.0249

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0110

Gnomad MID

AF:

0.00418

Gnomad NFE

AF:

0.00556

Gnomad OTH

AF:

0.00463

GnomAD3 exomes

AF:

0.00549

AC:

990

AN:

180366

Hom.:

AF XY:

0.00519

AC XY:

342

AN XY:

65906

show subpopulations

Gnomad AFR exome

AF:

0.000914

Gnomad AMR exome

AF:

0.00285

Gnomad ASJ exome

AF:

0.0261

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0120

Gnomad NFE exome

AF:

0.00618

Gnomad OTH exome

AF:

0.00688

GnomAD4 exome

AF:

0.00622

AC:

6826

AN:

1097054

Hom.:

Cov.:

AF XY:

0.00598

AC XY:

2168

AN XY:

362704

show subpopulations

Gnomad4 AFR exome

AF:

0.00114

Gnomad4 AMR exome

AF:

0.00233

Gnomad4 ASJ exome

AF:

0.0260

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000185

Gnomad4 FIN exome

AF:

0.0123

Gnomad4 NFE exome

AF:

0.00650

Gnomad4 OTH exome

AF:

0.00543

GnomAD4 genome

AF:

0.00441

AC:

496

AN:

112443

Hom.:

Cov.:

AF XY:

0.00439

AC XY:

152

AN XY:

34607

show subpopulations

Gnomad4 AFR

AF:

0.000806

Gnomad4 AMR

AF:

0.00316

Gnomad4 ASJ

AF:

0.0249

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0110

Gnomad4 NFE

AF:

0.00556

Gnomad4 OTH

AF:

0.00457

Alfa

AF:

0.00667

Hom.:

Bravo

AF:

0.00397

EpiCase

AF:

0.00545

EpiControl

AF:

0.00717

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

DANN

Benign

0.80

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

Details are displayed if max score is > 0.2

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