chr12-86748104-C-A

Variant names:

• chr12-86748104-C-A
• rs10492295
• ENST00000621808.5:c.-381-20863G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000621808.5(MGAT4C):​c.-381-20863G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: MGAT4C ENST00000621808.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 1 publications found

Genes affected

MGAT4C (HGNC:30871): (MGAT4 family member C) Predicted to enable acetylglucosaminyltransferase activity. Predicted to be involved in protein N-linked glycosylation. Predicted to be located in Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000258185 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGAT4C	NM_001351285.2	c.-326-20863G>T		intron_variant	Intron 1 of 8		NP_001338214.1
MGAT4C	NM_001351286.2	c.-261-20863G>T		intron_variant	Intron 1 of 7		NP_001338215.1
MGAT4C	NM_013244.5	c.-229+90562G>T		intron_variant	Intron 1 of 6		NP_037376.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGAT4C	ENST00000621808.5	c.-381-20863G>T		intron_variant	Intron 1 of 8	1		ENSP00000478300.1
MGAT4C	ENST00000548651.6	c.-261-20863G>T		intron_variant	Intron 1 of 7	5		ENSP00000447253.1
ENSG00000258185	ENST00000550014.1	n.334-20863G>T		intron_variant	Intron 1 of 2	5
MGAT4C	ENST00000551921.2	n.240-20863G>T		intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 10

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.70
DANN	Benign	0.13
PhyloP100		-0.23

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

Other links and lift over

dbSNP: rs10492295; hg19: chr12-87141881;