chr12-86657533-G-A

Variant names:

• chr12-86657533-G-A
• rs2195229
• ENST00000621808.5:c.-349+69676C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000621808.5(MGAT4C):​c.-349+69676C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0875 in 151,578 control chromosomes in the GnomAD database, including 948 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 0.088 (948 hom., cov: 32)
• Consequence: MGAT4C ENST00000621808.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855
• Publications: 2 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGAT4C	NM_001351285.2	c.-294+69676C>T		intron_variant	Intron 2 of 8		NP_001338214.1
MGAT4C	NM_001351286.2	c.-229+69676C>T		intron_variant	Intron 2 of 7		NP_001338215.1
MGAT4C	NM_013244.5	c.-229+181133C>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.-349+69676C>T		intron_variant	Intron 2 of 8	1		ENSP00000478300.1
MGAT4C	ENST00000548651.6	c.-229+69676C>T		intron_variant	Intron 2 of 7	5		ENSP00000447253.1
ENSG00000258185	ENST00000550014.1	n.367-57872C>T		intron_variant	Intron 2 of 2	5
MGAT4C	ENST00000551921.2	n.272+69676C>T		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.0874 AC: 13244 AN: 151456 Hom.: 944 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.0411

Gnomad ASJ AF: 0.0433

Gnomad EAS AF: 0.00271

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.0648

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.0502

Gnomad OTH AF: 0.0660

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

GnomAD4 genome AF: 0.0875 AC: 13265 AN: 151578 Hom.: 948 Cov.: 32 AF XY: 0.0851 AC XY: 6302 AN XY: 74040

African (AFR) AF: 0.196 AC: 8103 AN: 41388

American (AMR) AF: 0.0411 AC: 623 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.0433 AC: 150 AN: 3466

East Asian (EAS) AF: 0.00272 AC: 14 AN: 5152

South Asian (SAS) AF: 0.0141 AC: 68 AN: 4816

European-Finnish (FIN) AF: 0.0648 AC: 681 AN: 10512

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0502 AC: 3402 AN: 67756

Other (OTH) AF: 0.0653 AC: 138 AN: 2112

Alfa AF: 0.0554 Hom.: 181

Bravo AF: 0.0892

Asia WGS AF: 0.0240 AC: 83 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.51
PhyloP100		-0.85
Mutation Taster		=100/0	polymorphism (auto)

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: rs2195229; hg19: chr12-87051310;