Variant 21-43959714-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_020132.5(AGPAT3):c.33C>T(p.Phe11=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00465 in 1,613,748 control chromosomes in the GnomAD database, including 46 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0033 ( 3 hom., cov: 33)

Exomes 𝑓: 0.0048 ( 43 hom. )

Consequence

AGPAT3
NM_020132.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.39

Variant links:

Genes affected

AGPAT3 (HGNC:326): (1-acylglycerol-3-phosphate O-acyltransferase 3) The protein encoded by this gene is an acyltransferase that converts lysophosphatidic acid into phosphatidic acid, which is the second step in the de novo phospholipid biosynthetic pathway. The encoded protein may be an integral membrane protein. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

AGPAT3 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 21-43959714-C-T is Benign according to our data. Variant chr21-43959714-C-T is described in ClinVar as [Benign]. Clinvar id is 2652727.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=1.39 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGPAT3	NM_020132.5 linkuse as main transcript	c.33C>T	p.Phe11=	synonymous_variant	3/10	ENST00000291572.13	NP_064517.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AGPAT3	ENST00000291572.13 linkuse as main transcript	c.33C>T	p.Phe11=	synonymous_variant	3/10	1	NM_020132.5	ENSP00000291572	P1	Q9NRZ7-1
	ENST00000674444.1 linkuse as main transcript			downstream_gene_variant				ENSP00000501503	P1

Frequencies

GnomAD3 genomes

AF:

0.00333

AC:

507

AN:

152176

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000773

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00150

Gnomad ASJ

AF:

0.0173

Gnomad EAS

AF:

0.000769

Gnomad SAS

AF:

0.0141

Gnomad FIN

AF:

0.00263

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00412

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.00496

AC:

1247

AN:

251240

Hom.:

AF XY:

0.00549

AC XY:

746

AN XY:

135830

show subpopulations

Gnomad AFR exome

AF:

0.000369

Gnomad AMR exome

AF:

0.00234

Gnomad ASJ exome

AF:

0.0170

Gnomad EAS exome

AF:

0.000924

Gnomad SAS exome

AF:

0.0122

Gnomad FIN exome

AF:

0.00335

Gnomad NFE exome

AF:

0.00433

Gnomad OTH exome

AF:

0.00554

GnomAD4 exome

AF:

0.00478

AC:

6988

AN:

1461454

Hom.:

Cov.:

AF XY:

0.00511

AC XY:

3717

AN XY:

727080

show subpopulations

Gnomad4 AFR exome

AF:

0.000657

Gnomad4 AMR exome

AF:

0.00221

Gnomad4 ASJ exome

AF:

0.0182

Gnomad4 EAS exome

AF:

0.000378

Gnomad4 SAS exome

AF:

0.0123

Gnomad4 FIN exome

AF:

0.00350

Gnomad4 NFE exome

AF:

0.00427

Gnomad4 OTH exome

AF:

0.00512

GnomAD4 genome

AF:

0.00334

AC:

508

AN:

152294

Hom.:

Cov.:

AF XY:

0.00348

AC XY:

259

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.000770

Gnomad4 AMR

AF:

0.00150

Gnomad4 ASJ

AF:

0.0173

Gnomad4 EAS

AF:

0.000771

Gnomad4 SAS

AF:

0.0141

Gnomad4 FIN

AF:

0.00263

Gnomad4 NFE

AF:

0.00413

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00494

Hom.:

Bravo

AF:

0.00286

Asia WGS

AF:

0.00693

AC:

AN:

3478

EpiCase

AF:

0.00474

EpiControl

AF:

0.00409

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

AGPAT3: BP4, BP7, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

DANN

Benign

0.76

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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