4-102632290-GAA-GAAAA

Variant names:

• chr4-102632290-G-GAA
• NM_005908.4:c.2416-11_2416-10dupTT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_005908.4(MANBA):​c.2416-11_2416-10dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0000097 (0 hom.)
• Consequence: MANBA NM_005908.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MANBA	NM_005908.4	c.2416-11_2416-10dupTT		intron_variant	Intron 16 of 16	ENST00000647097.2	NP_005899.3
MANBA	XM_047415692.1	c.2341-11_2341-10dupTT		intron_variant	Intron 17 of 17		XP_047271648.1
MANBA	XM_047415693.1	c.2341-11_2341-10dupTT		intron_variant	Intron 17 of 17		XP_047271649.1
MANBA	XM_047415694.1	c.1768-11_1768-10dupTT		intron_variant	Intron 12 of 12		XP_047271650.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MANBA	ENST00000647097.2	c.2416-10_2416-9insTT		intron_variant	Intron 16 of 16		NM_005908.4	ENSP00000495247.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000966 AC: 12 AN: 1242520 Hom.: 0 Cov.: 0 AF XY: 0.00000802 AC XY: 5 AN XY: 623664

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000118

Gnomad4 OTH exome AF: 0.0000192

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr4-103553447;