4-102631656-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.824

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]

ACMG classification

Verdict is Benign. Variant got -14 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_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MANBA	ENST00000647097.2	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.: 31

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.: 0 AF XY: 0.510 AC XY: 76232 AN XY: 149530

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.: 31 AF XY: 0.549 AC XY: 40709 AN XY: 74188

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:1

Revision: criteria provided, single submitter

Submissions by phenotype

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

Other links and lift over

dbSNP: rs4013; hg19: chr4-103552813; COSMIC: COSV105051649; COSMIC: COSV105051649;