Variant 6-32168770-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006411.4(AGPAT1):c.*506A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 155,158 control chromosomes in the GnomAD database, including 31,887 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 0.64 ( 31367 hom., cov: 31)

Exomes 𝑓: 0.55 ( 520 hom. )

Consequence

AGPAT1
NM_006411.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.29

Variant links:

Genes affected

AGPAT1 (HGNC:324): (1-acylglycerol-3-phosphate O-acyltransferase 1) This gene encodes an enzyme that converts lysophosphatidic acid (LPA) into phosphatidic acid (PA). LPA and PA are two phospholipids involved in signal transduction and in lipid biosynthesis in cells. This enzyme localizes to the endoplasmic reticulum. This gene is located in the class III region of the human major histocompatibility complex. Alternative splicing results in two transcript variants encoding the same protein. [provided by RefSeq, Jul 2008]

AGPAT1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGPAT1	NM_006411.4 linkuse as main transcript	c.*506A>C		3_prime_UTR_variant	7/7	ENST00000375107.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGPAT1	ENST00000375107.8 linkuse as main transcript	c.*506A>C		3_prime_UTR_variant	7/7	1	NM_006411.4	P1

Frequencies

GnomAD3 genomes

AF:

0.641

AC:

97273

AN:

151750

Hom.:

31352

Cov.:

show subpopulations

Gnomad AFR

AF:

0.675

Gnomad AMI

AF:

0.704

Gnomad AMR

AF:

0.631

Gnomad ASJ

AF:

0.747

Gnomad EAS

AF:

0.585

Gnomad SAS

AF:

0.685

Gnomad FIN

AF:

0.574

Gnomad MID

AF:

0.778

Gnomad NFE

AF:

0.626

Gnomad OTH

AF:

0.685

GnomAD4 exome

AF:

0.550

AC:

1808

AN:

3288

Hom.:

520

Cov.:

AF XY:

0.560

AC XY:

959

AN XY:

1712

show subpopulations

Gnomad4 AFR exome

AF:

0.630

Gnomad4 AMR exome

AF:

0.505

Gnomad4 ASJ exome

AF:

0.543

Gnomad4 EAS exome

AF:

0.423

Gnomad4 SAS exome

AF:

0.665

Gnomad4 FIN exome

AF:

0.536

Gnomad4 NFE exome

AF:

0.559

Gnomad4 OTH exome

AF:

0.552

GnomAD4 genome

AF:

0.641

AC:

97347

AN:

151870

Hom.:

31367

Cov.:

AF XY:

0.640

AC XY:

47489

AN XY:

74226

show subpopulations

Gnomad4 AFR

AF:

0.675

Gnomad4 AMR

AF:

0.631

Gnomad4 ASJ

AF:

0.747

Gnomad4 EAS

AF:

0.585

Gnomad4 SAS

AF:

0.684

Gnomad4 FIN

AF:

0.574

Gnomad4 NFE

AF:

0.626

Gnomad4 OTH

AF:

0.687

Alfa

AF:

0.643

Hom.:

47257

Bravo

AF:

0.649

Asia WGS

AF:

0.666

AC:

2320

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

DANN

Benign

0.72

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over