6-20171857-T-G

Position:

• chr6-20171857-T-G

Variant summary

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

The ENST00000324607.8(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 ENST00000324607.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MBOAT1	NM_001080480.3	c.100-19088A>C		intron_variant		ENST00000324607.8	NP_001073949.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MBOAT1	ENST00000324607.8	c.100-19088A>C		intron_variant		1	NM_001080480.3	ENSP00000324944	P1

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

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.840

Gnomad4 ASJ AF: 0.871

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.761

Gnomad4 FIN AF: 0.907

Gnomad4 NFE AF: 0.884

Gnomad4 OTH AF: 0.856

Alfa AF: 0.874 Hom.: 12453

Bravo AF: 0.861

Asia WGS AF: 0.702 AC: 2443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.72

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: rs694094; hg19: chr6-20172088;