NM_001080480.3:c.324-1635C>T

Variant names:

• chr6-20145950-G-A
• rs2148943
• NM_001080480.3:c.324-1635C>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.324-1635C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,036 control chromosomes in the GnomAD database, including 4,428 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 0.22 (4428 hom., cov: 33)
• Consequence: MBOAT1 NM_001080480.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MBOAT1	NM_001080480.3	c.324-1635C>T		intron_variant	Intron 3 of 12	ENST00000324607.8	NP_001073949.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MBOAT1	ENST00000324607.8	c.324-1635C>T		intron_variant	Intron 3 of 12	1	NM_001080480.3	ENSP00000324944.7

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33825 AN: 151918 Hom.: 4421 Cov.: 33

Gnomad AFR AF: 0.0912

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.223 AC: 33842 AN: 152036 Hom.: 4428 Cov.: 33 AF XY: 0.223 AC XY: 16597 AN XY: 74314

African (AFR) AF: 0.0912 AC: 3784 AN: 41496

American (AMR) AF: 0.276 AC: 4216 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 976 AN: 3470

East Asian (EAS) AF: 0.478 AC: 2467 AN: 5162

South Asian (SAS) AF: 0.224 AC: 1076 AN: 4812

European-Finnish (FIN) AF: 0.211 AC: 2216 AN: 10522

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18364 AN: 67972

Other (OTH) AF: 0.236 AC: 497 AN: 2110

Alfa AF: 0.260 Hom.: 5672

Bravo AF: 0.223

Asia WGS AF: 0.357 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.0
DANN	Benign	0.41
PhyloP100		0.43
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: rs2148943; hg19: chr6-20146181;