chr6-20184820-A-G

Variant names:

• chr6-20184820-A-G
• rs555017
• NM_001080480.3:c.99+27316T>C

Variant summary

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

The NM_001080480.3(MBOAT1):​c.99+27316T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 151,118 control chromosomes in the GnomAD database, including 25,698 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 0.57 (25698 hom., cov: 28)
• Consequence: MBOAT1 NM_001080480.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 9 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 (AMR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MBOAT1	NM_001080480.3	c.99+27316T>C		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.99+27316T>C		intron_variant	Intron 1 of 12	1	NM_001080480.3	ENSP00000324944.7

Frequencies

GnomAD3 genomes AF: 0.574 AC: 86613 AN: 151000 Hom.: 25669 Cov.: 28

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.574 AC: 86698 AN: 151118 Hom.: 25698 Cov.: 28 AF XY: 0.575 AC XY: 42379 AN XY: 73724

African (AFR) AF: 0.426 AC: 17529 AN: 41114

American (AMR) AF: 0.675 AC: 10256 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2033 AN: 3464

East Asian (EAS) AF: 0.557 AC: 2843 AN: 5108

South Asian (SAS) AF: 0.451 AC: 2163 AN: 4792

European-Finnish (FIN) AF: 0.681 AC: 7030 AN: 10316

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42807 AN: 67842

Other (OTH) AF: 0.573 AC: 1205 AN: 2104

Alfa AF: 0.614 Hom.: 46818

Bravo AF: 0.572

Asia WGS AF: 0.482 AC: 1680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.73
PhyloP100		1.1
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: rs555017; hg19: chr6-20185051;