rs843319

Variant names:

• chr6-20135594-G-A
• rs843319
• NM_001080480.3:c.420-4395C>T

Variant summary

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

The NM_001080480.3(MBOAT1):​c.420-4395C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 152,008 control chromosomes in the GnomAD database, including 25,530 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 0.54 (25530 hom., cov: 32)
• Consequence: MBOAT1 NM_001080480.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080480.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MBOAT1	NM_001080480.3	MANE Select	c.420-4395C>T		intron	N/A	NP_001073949.1	Q6ZNC8-1
	MBOAT1	NR_073465.2		n.431-6841C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MBOAT1	ENST00000324607.8	TSL:1 MANE Select	c.420-4395C>T		intron	N/A	ENSP00000324944.7	Q6ZNC8-1
	MBOAT1	ENST00000969078.1		c.447-4395C>T		intron	N/A	ENSP00000639137.1
	MBOAT1	ENST00000883939.1		c.420-4395C>T		intron	N/A	ENSP00000553998.1

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82588 AN: 151890 Hom.: 25530 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.543 AC: 82596 AN: 152008 Hom.: 25530 Cov.: 32 AF XY: 0.548 AC XY: 40703 AN XY: 74284

African (AFR) AF: 0.237 AC: 9811 AN: 41436

American (AMR) AF: 0.509 AC: 7766 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2347 AN: 3470

East Asian (EAS) AF: 0.495 AC: 2559 AN: 5168

South Asian (SAS) AF: 0.624 AC: 3005 AN: 4816

European-Finnish (FIN) AF: 0.744 AC: 7857 AN: 10562

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47252 AN: 67982

Other (OTH) AF: 0.556 AC: 1176 AN: 2114

Alfa AF: 0.643 Hom.: 145510

Bravo AF: 0.509

Asia WGS AF: 0.512 AC: 1777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.0
DANN	Benign	0.53
PhyloP100		0.20
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: rs843319; hg19: chr6-20135825;