Variant chr4-102631656-C-T 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_005908.4(MANBA):c.*401G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 446,354 control chromosomes in the GnomAD database, including 62,577 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.55 ( 23352 hom., cov: 31)

Exomes 𝑓: 0.51 ( 39225 hom. )

Consequence

MANBA
NM_005908.4 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.824

Variant links:

Genes affected

MANBA (HGNC:6831): (mannosidase beta) This gene encodes a member of the glycosyl hydrolase 2 family. The encoded protein localizes to the lysosome where it is the final exoglycosidase in the pathway for N-linked glycoprotein oligosaccharide catabolism. Mutations in this gene are associated with beta-mannosidosis, a lysosomal storage disease that has a wide spectrum of neurological involvement. [provided by RefSeq, Jul 2008]

MANBA 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=-0.91).

BP6

Variant 4-102631656-C-T is Benign according to our data. Variant chr4-102631656-C-T is described in ClinVar as [Benign]. Clinvar id is 347067.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
MANBA	NM_005908.4 linkuse as main transcript	c.*401G>A	3_prime_UTR_variant	17/17	ENST00000647097.2
MANBA	XM_047415692.1 linkuse as main transcript	c.*401G>A	3_prime_UTR_variant	18/18
MANBA	XM_047415693.1 linkuse as main transcript	c.*401G>A	3_prime_UTR_variant	18/18
MANBA	XM_047415694.1 linkuse as main transcript	c.*401G>A	3_prime_UTR_variant	13/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MANBA	ENST00000647097.2 linkuse as main transcript	c.*401G>A		3_prime_UTR_variant	17/17		NM_005908.4	P1

Frequencies

GnomAD3 genomes

AF:

0.550

AC:

83362

AN:

151672

Hom.:

23315

Cov.:

show subpopulations

Gnomad AFR

AF:

0.631

Gnomad AMI

AF:

0.577

Gnomad AMR

AF:

0.615

Gnomad ASJ

AF:

0.509

Gnomad EAS

AF:

0.518

Gnomad SAS

AF:

0.452

Gnomad FIN

AF:

0.473

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.508

Gnomad OTH

AF:

0.557

GnomAD4 exome

AF:

0.511

AC:

150553

AN:

294564

Hom.:

39225

Cov.:

AF XY:

0.510

AC XY:

76232

AN XY:

149530

show subpopulations

Gnomad4 AFR exome

AF:

0.618

Gnomad4 AMR exome

AF:

0.675

Gnomad4 ASJ exome

AF:

0.490

Gnomad4 EAS exome

AF:

0.479

Gnomad4 SAS exome

AF:

0.435

Gnomad4 FIN exome

AF:

0.471

Gnomad4 NFE exome

AF:

0.508

Gnomad4 OTH exome

AF:

0.535

GnomAD4 genome

AF:

0.550

AC:

83446

AN:

151790

Hom.:

23352

Cov.:

AF XY:

0.549

AC XY:

40709

AN XY:

74188

show subpopulations

Gnomad4 AFR

AF:

0.631

Gnomad4 AMR

AF:

0.616

Gnomad4 ASJ

AF:

0.509

Gnomad4 EAS

AF:

0.518

Gnomad4 SAS

AF:

0.452

Gnomad4 FIN

AF:

0.473

Gnomad4 NFE

AF:

0.508

Gnomad4 OTH

AF:

0.550

Alfa

AF:

0.521

Hom.:

20064

Bravo

AF:

0.567

Asia WGS

AF:

0.506

AC:

1755

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

- -

Beta-D-mannosidosis

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 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

-0.91

CADD

Benign

0.23

DANN

Benign

0.60

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