6-20155943-T-C

Variant names:

• chr6-20155943-T-C
• rs1202199
• NM_001080480.3:c.100-3174A>G

Variant summary

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

The NM_001080480.3(MBOAT1):​c.100-3174A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 152,180 control chromosomes in the GnomAD database, including 58,547 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 0.87 (58547 hom., cov: 32)
• Consequence: MBOAT1 NM_001080480.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 11 publications found

Genes affected

MBOAT1 (HGNC:21579): (membrane bound O-acyltransferase domain containing 1) This gene belongs to the membrane-bound O-acetyltransferase superfamily. The encoded transmembrane protein is an enzyme that transfers organic compounds, preferably from oleoyl-CoA, to hydroxyl groups of protein targets in membranes. A translocation disrupting this gene may be associated with brachydactyly syndactyly syndrome. Alternately spliced transcript variants have been described for this gene. [provided by RefSeq, Nov 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MBOAT1	NM_001080480.3	c.100-3174A>G		intron_variant	Intron 1 of 12	ENST00000324607.8	NP_001073949.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MBOAT1	ENST00000324607.8	c.100-3174A>G		intron_variant	Intron 1 of 12	1	NM_001080480.3	ENSP00000324944.7

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133012 AN: 152062 Hom.: 58514 Cov.: 32

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.875 AC: 133100 AN: 152180 Hom.: 58547 Cov.: 32 AF XY: 0.877 AC XY: 65249 AN XY: 74410

African (AFR) AF: 0.787 AC: 32668 AN: 41494

American (AMR) AF: 0.911 AC: 13917 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2982 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5157 AN: 5178

South Asian (SAS) AF: 0.880 AC: 4247 AN: 4828

European-Finnish (FIN) AF: 0.926 AC: 9812 AN: 10598

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.904 AC: 61501 AN: 68022

Other (OTH) AF: 0.887 AC: 1867 AN: 2106

Alfa AF: 0.899 Hom.: 117725

Bravo AF: 0.871

Asia WGS AF: 0.932 AC: 3242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.3
DANN	Benign	0.77
PhyloP100		-0.93
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: rs1202199; hg19: chr6-20156174;