chr6-20184820-A-G

Position:

• chr6-20184820-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.88).
• 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/exons	MANE	Protein	UniProt
MBOAT1	NM_001080480.3	c.99+27316T>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.99+27316T>C		intron_variant		1	NM_001080480.3	ENSP00000324944	P1

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

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.573

Alfa AF: 0.616 Hom.: 39542

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

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: rs555017; hg19: chr6-20185051;