6-20155943-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MBOAT1	NM_001080480.3	c.100-3174A>G		intron_variant		ENST00000324607.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MBOAT1	ENST00000324607.8	c.100-3174A>G		intron_variant		1	NM_001080480.3	P1

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

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.911

Gnomad4 ASJ AF: 0.859

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.926

Gnomad4 NFE AF: 0.904

Gnomad4 OTH AF: 0.887

Alfa AF: 0.900 Hom.: 92024

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1202199; hg19: chr6-20156174;