Variant chr4-102759827-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005908.4(MANBA):c.177+891T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,940 control chromosomes in the GnomAD database, including 12,064 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.40 ( 12064 hom., cov: 32)

Consequence

MANBA
NM_005908.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.24

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
MANBA	NM_005908.4 link	c.177+891T>C	intron_variant	ENST00000647097.2	NP_005899.3	O00462
MANBA	XM_047415692.1 link	c.-3368+891T>C	intron_variant		XP_047271648.1
MANBA	XM_047415693.1 link	c.-3368+497T>C	intron_variant		XP_047271649.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MANBA	ENST00000647097.2 link	c.177+891T>C		intron_variant			NM_005908.4	ENSP00000495247.1		O00462

Frequencies

GnomAD3 genomes

AF:

0.396

AC:

60186

AN:

151822

Hom.:

12051

Cov.:

show subpopulations

Gnomad AFR

AF:

0.443

Gnomad AMI

AF:

0.322

Gnomad AMR

AF:

0.450

Gnomad ASJ

AF:

0.409

Gnomad EAS

AF:

0.385

Gnomad SAS

AF:

0.370

Gnomad FIN

AF:

0.407

Gnomad MID

AF:

0.443

Gnomad NFE

AF:

0.357

Gnomad OTH

AF:

0.411

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.396

AC:

60235

AN:

151940

Hom.:

12064

Cov.:

AF XY:

0.400

AC XY:

29699

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.442

Gnomad4 AMR

AF:

0.451

Gnomad4 ASJ

AF:

0.409

Gnomad4 EAS

AF:

0.386

Gnomad4 SAS

AF:

0.368

Gnomad4 FIN

AF:

0.407

Gnomad4 NFE

AF:

0.357

Gnomad4 OTH

AF:

0.407

Alfa

AF:

0.373

Hom.:

9882

Bravo

AF:

0.402

Asia WGS

AF:

0.377

AC:

1311

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

DANN

Benign

0.66

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over