Variant chr19-54174203-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000245615.6(MBOAT7):c.1260C>T(p.Ala420=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 1,597,250 control chromosomes in the GnomAD database, including 14,562 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 2333 hom., cov: 32)

Exomes 𝑓: 0.13 ( 12229 hom. )

Consequence

MBOAT7
ENST00000245615.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.34

Variant links:

Genes affected

MBOAT7 (HGNC:15505): (membrane bound O-acyltransferase domain containing 7) This gene encodes a member of the membrane-bound O-acyltransferases family of integral membrane proteins that have acyltransferase activity. The encoded protein is a lysophosphatidylinositol acyltransferase that has specificity for arachidonoyl-CoA as an acyl donor. This protein is involved in the reacylation of phospholipids as part of the phospholipid remodeling pathway known as the Land cycle. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2009]

MBOAT7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 19-54174203-G-A is Benign according to our data. Variant chr19-54174203-G-A is described in ClinVar as [Benign]. Clinvar id is 1262088.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.34 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MBOAT7	NM_024298.5 linkuse as main transcript	c.1260C>T	p.Ala420=	synonymous_variant	8/8	ENST00000245615.6	NP_077274.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MBOAT7	ENST00000245615.6 linkuse as main transcript	c.1260C>T	p.Ala420=	synonymous_variant	8/8	1	NM_024298.5	ENSP00000245615	P1	Q96N66-1

Frequencies

GnomAD3 genomes

AF:

0.163

AC:

24785

AN:

151974

Hom.:

2326

Cov.:

show subpopulations

Gnomad AFR

AF:

0.257

Gnomad AMI

AF:

0.110

Gnomad AMR

AF:

0.143

Gnomad ASJ

AF:

0.0784

Gnomad EAS

AF:

0.129

Gnomad SAS

AF:

0.202

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.158

GnomAD3 exomes

AF:

0.144

AC:

34558

AN:

240374

Hom.:

2688

AF XY:

0.143

AC XY:

18596

AN XY:

130182

show subpopulations

Gnomad AFR exome

AF:

0.263

Gnomad AMR exome

AF:

0.153

Gnomad ASJ exome

AF:

0.0877

Gnomad EAS exome

AF:

0.132

Gnomad SAS exome

AF:

0.193

Gnomad FIN exome

AF:

0.116

Gnomad NFE exome

AF:

0.123

Gnomad OTH exome

AF:

0.133

GnomAD4 exome

AF:

0.126

AC:

182419

AN:

1445158

Hom.:

12229

Cov.:

AF XY:

0.128

AC XY:

91862

AN XY:

717286

show subpopulations

Gnomad4 AFR exome

AF:

0.257

Gnomad4 AMR exome

AF:

0.153

Gnomad4 ASJ exome

AF:

0.0858

Gnomad4 EAS exome

AF:

0.138

Gnomad4 SAS exome

AF:

0.192

Gnomad4 FIN exome

AF:

0.115

Gnomad4 NFE exome

AF:

0.117

Gnomad4 OTH exome

AF:

0.130

GnomAD4 genome

AF:

0.163

AC:

24830

AN:

152092

Hom.:

2333

Cov.:

AF XY:

0.164

AC XY:

12212

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.258

Gnomad4 AMR

AF:

0.143

Gnomad4 ASJ

AF:

0.0784

Gnomad4 EAS

AF:

0.129

Gnomad4 SAS

AF:

0.203

Gnomad4 FIN

AF:

0.113

Gnomad4 NFE

AF:

0.123

Gnomad4 OTH

AF:

0.157

Alfa

AF:

0.130

Hom.:

2048

Bravo

AF:

0.170

Asia WGS

AF:

0.143

AC:

499

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 16, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.20

DANN

Benign

0.66

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over