Variant chr1-11273485-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_013319.3(UBIAD1):c.-47T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0106 in 1,608,588 control chromosomes in the GnomAD database, including 1,439 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.054 ( 732 hom., cov: 31)

Exomes 𝑓: 0.0061 ( 707 hom. )

Consequence

UBIAD1
NM_013319.3 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.822

Variant links:

Genes affected

UBIAD1 (HGNC:30791): (UbiA prenyltransferase domain containing 1) This gene encodes a protein thought to be involved in cholesterol and phospholipid metabolism. Mutations in this gene are associated with Schnyder crystalline corneal dystrophy. [provided by RefSeq, Oct 2008]

UBIAD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BP6

Variant 1-11273485-T-G is Benign according to our data. Variant chr1-11273485-T-G is described in ClinVar as [Benign]. Clinvar id is 291818.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
UBIAD1	NM_013319.3 linkuse as main transcript	c.-47T>G	5_prime_UTR_variant	1/2	ENST00000376810.6	NP_037451.1
UBIAD1	NM_001330349.2 linkuse as main transcript	c.-47T>G	5_prime_UTR_variant	1/3		NP_001317278.1
UBIAD1	NM_001330350.2 linkuse as main transcript	c.-47T>G	5_prime_UTR_variant	1/2		NP_001317279.1
UBIAD1	XM_047418727.1 linkuse as main transcript	c.-47T>G	5_prime_UTR_variant	1/3		XP_047274683.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBIAD1	ENST00000376810.6 linkuse as main transcript	c.-47T>G		5_prime_UTR_variant	1/2	1	NM_013319.3	ENSP00000366006	P1	Q9Y5Z9-1
UBIAD1	ENST00000376804.2 linkuse as main transcript			upstream_gene_variant		2		ENSP00000366000		Q9Y5Z9-2

Frequencies

GnomAD3 genomes

AF:

0.0541

AC:

8235

AN:

152160

Hom.:

726

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0211

Gnomad ASJ

AF:

0.0156

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.000823

Gnomad OTH

AF:

0.0421

GnomAD3 exomes

AF:

0.0141

AC:

3417

AN:

242416

Hom.:

264

AF XY:

0.0109

AC XY:

1445

AN XY:

132618

show subpopulations

Gnomad AFR exome

AF:

0.190

Gnomad AMR exome

AF:

0.00939

Gnomad ASJ exome

AF:

0.0190

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000230

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000769

Gnomad OTH exome

AF:

0.00838

GnomAD4 exome

AF:

0.00608

AC:

8852

AN:

1456310

Hom.:

707

Cov.:

AF XY:

0.00531

AC XY:

3850

AN XY:

724398

show subpopulations

Gnomad4 AFR exome

AF:

0.196

Gnomad4 AMR exome

AF:

0.0110

Gnomad4 ASJ exome

AF:

0.0165

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000349

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000416

Gnomad4 OTH exome

AF:

0.0142

GnomAD4 genome

AF:

0.0543

AC:

8271

AN:

152278

Hom.:

732

Cov.:

AF XY:

0.0520

AC XY:

3869

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.186

Gnomad4 AMR

AF:

0.0211

Gnomad4 ASJ

AF:

0.0156

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000823

Gnomad4 OTH

AF:

0.0416

Alfa

AF:

0.0227

Hom.:

Bravo

AF:

0.0626

Asia WGS

AF:

0.0120

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Schnyder crystalline corneal dystrophy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

7.2

DANN

Benign

0.81

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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