17-76872847-GC-AT

Variant names:

• chr17-76872847-GC-AT
• ENST00000428789.6:c.98_99delGCinsAT
• MGAT5B p.Arg33His

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_198955.1(MGAT5B):​c.98_99delGCinsAT​(p.Arg33His) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R33C) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MGAT5B NM_198955.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.26
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198955.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAT5B	NM_001199172.2	MANE Select	c.69-4_69-3delGCinsAT		splice_region intron	N/A	NP_001186101.1	Q3V5L5-1
	MGAT5B	NM_198955.1		c.98_99delGCinsAT	p.Arg33His	missense	N/A	NP_945193.1	Q3V5L5-2
	MGAT5B	NM_144677.3		c.69-4_69-3delGCinsAT		splice_region intron	N/A	NP_653278.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAT5B	ENST00000428789.6	TSL:1	c.98_99delGCinsAT	p.Arg33His	missense	N/A	ENSP00000391227.2	Q3V5L5-2
	MGAT5B	ENST00000569840.7	TSL:5 MANE Select	c.69-4_69-3delGCinsAT		splice_region intron	N/A	ENSP00000456037.2	Q3V5L5-1
	MGAT5B	ENST00000565675.1	TSL:1	c.69-4_69-3delGCinsAT		splice_region intron	N/A	ENSP00000457614.1	H3BR20

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr17-74868929;