17-76899704-A-C

Position:

• chr17-76899704-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001199172.2(MGAT5B):​c.330-2851A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,854 control chromosomes in the GnomAD database, including 11,205 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 0.37 (11205 hom., cov: 31)
• Consequence: MGAT5B NM_001199172.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.903

Genes affected

MGAT5B (HGNC:24140): (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B) Enables alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity and manganese ion binding activity. Involved in protein O-linked glycosylation via serine. Predicted to be located in Golgi membrane. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MGAT5B	NM_001199172.2	c.330-2851A>C		intron_variant		ENST00000569840.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGAT5B	ENST00000569840.7	c.330-2851A>C		intron_variant		5	NM_001199172.2	A1

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56290 AN: 151736 Hom.: 11200 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.371 AC: 56320 AN: 151854 Hom.: 11205 Cov.: 31 AF XY: 0.376 AC XY: 27880 AN XY: 74236

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.394

Alfa AF: 0.353 Hom.: 4855

Bravo AF: 0.374

Asia WGS AF: 0.642 AC: 2228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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

Other links and lift over

dbSNP: rs9916886; hg19: chr17-74895786;