6-20171857-T-G

Variant names:

• chr6-20171857-T-G
• rs694094
• NM_001080480.3:c.100-19088A>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.100-19088A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.868 in 151,866 control chromosomes in the GnomAD database, including 57,318 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 (57318 hom., cov: 29)
• Consequence: MBOAT1 NM_001080480.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.878 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MBOAT1	NM_001080480.3	MANE Select	c.100-19088A>C		intron	N/A	NP_001073949.1
	MBOAT1	NR_073465.2		n.335-27542A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MBOAT1	ENST00000324607.8	TSL:1 MANE Select	c.100-19088A>C		intron	N/A	ENSP00000324944.7

Frequencies

GnomAD3 genomes AF: 0.868 AC: 131681 AN: 151748 Hom.: 57265 Cov.: 29

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.830

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.856

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

GnomAD4 genome AF: 0.868 AC: 131793 AN: 151866 Hom.: 57318 Cov.: 29 AF XY: 0.865 AC XY: 64177 AN XY: 74192

African (AFR) AF: 0.883 AC: 36552 AN: 41406

American (AMR) AF: 0.840 AC: 12819 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3019 AN: 3468

East Asian (EAS) AF: 0.634 AC: 3207 AN: 5056

South Asian (SAS) AF: 0.761 AC: 3661 AN: 4810

European-Finnish (FIN) AF: 0.907 AC: 9592 AN: 10570

Middle Eastern (MID) AF: 0.838 AC: 243 AN: 290

European-Non Finnish (NFE) AF: 0.884 AC: 60116 AN: 67984

Other (OTH) AF: 0.856 AC: 1806 AN: 2110

Alfa AF: 0.871 Hom.: 14128

Bravo AF: 0.861

Asia WGS AF: 0.702 AC: 2443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.72
PhyloP100		-0.75
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: rs694094; hg19: chr6-20172088;