rs16883399

Positions:

• chr6-20130804-A-G
• chr6-20130804-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080480.3(MBOAT1):​c.475+340T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,232 control chromosomes in the GnomAD database, including 3,797 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 0.20 (3797 hom., cov: 33)
• Consequence: MBOAT1 NM_001080480.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.674

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=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MBOAT1	NM_001080480.3	c.475+340T>C		intron_variant		ENST00000324607.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MBOAT1	ENST00000324607.8	c.475+340T>C		intron_variant		1	NM_001080480.3	P1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29894 AN: 152114 Hom.: 3783 Cov.: 33

Gnomad AFR AF: 0.0562

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.196 AC: 29913 AN: 152232 Hom.: 3797 Cov.: 33 AF XY: 0.199 AC XY: 14809 AN XY: 74428

Gnomad4 AFR AF: 0.0561

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.221

Alfa AF: 0.216 Hom.: 2338

Bravo AF: 0.201

Asia WGS AF: 0.379 AC: 1318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	12
DANN	Benign	0.84

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: rs16883399; hg19: chr6-20131035;