Variant rs7162607 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_153613.3(LPCAT4):c.*342C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 154,470 control chromosomes in the GnomAD database, including 18,832 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 0.49 ( 18578 hom., cov: 31)

Exomes 𝑓: 0.44 ( 254 hom. )

Consequence

LPCAT4
NM_153613.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.694

Variant links:

Genes affected

LPCAT4 (HGNC:30059): (lysophosphatidylcholine acyltransferase 4) Members of the 1-acylglycerol-3-phosphate O-acyltransferase (EC 2.3.1.51) family, such as AGPAT7, catalyze the conversion of lysophosphatidic acid (LPA) to phosphatidic acid (PA), a precursor in the biosynthesis of all glycerolipids. Both LPA and PA are involved in signal transduction (Ye et al., 2005 [PubMed 16243729]).[supplied by OMIM, May 2008]

LPCAT4 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPCAT4	NM_153613.3 linkuse as main transcript	c.*342C>T		3_prime_UTR_variant	14/14	ENST00000314891.11	NP_705841.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPCAT4	ENST00000314891.11 linkuse as main transcript	c.*342C>T		3_prime_UTR_variant	14/14	1	NM_153613.3	ENSP00000317300	P1

Frequencies

GnomAD3 genomes

AF:

0.491

AC:

74592

AN:

151826

Hom.:

18563

Cov.:

show subpopulations

Gnomad AFR

AF:

0.574

Gnomad AMI

AF:

0.624

Gnomad AMR

AF:

0.529

Gnomad ASJ

AF:

0.459

Gnomad EAS

AF:

0.504

Gnomad SAS

AF:

0.458

Gnomad FIN

AF:

0.427

Gnomad MID

AF:

0.468

Gnomad NFE

AF:

0.445

Gnomad OTH

AF:

0.460

GnomAD4 exome

AF:

0.438

AC:

1107

AN:

2526

Hom.:

254

Cov.:

AF XY:

0.430

AC XY:

708

AN XY:

1648

show subpopulations

Gnomad4 AFR exome

AF:

0.778

Gnomad4 AMR exome

AF:

0.538

Gnomad4 ASJ exome

AF:

0.357

Gnomad4 EAS exome

AF:

0.418

Gnomad4 SAS exome

AF:

0.375

Gnomad4 FIN exome

AF:

0.462

Gnomad4 NFE exome

AF:

0.425

Gnomad4 OTH exome

AF:

0.456

GnomAD4 genome

AF:

0.491

AC:

74662

AN:

151944

Hom.:

18578

Cov.:

AF XY:

0.490

AC XY:

36353

AN XY:

74234

show subpopulations

Gnomad4 AFR

AF:

0.574

Gnomad4 AMR

AF:

0.530

Gnomad4 ASJ

AF:

0.459

Gnomad4 EAS

AF:

0.504

Gnomad4 SAS

AF:

0.457

Gnomad4 FIN

AF:

0.427

Gnomad4 NFE

AF:

0.445

Gnomad4 OTH

AF:

0.460

Alfa

AF:

0.462

Hom.:

9907

Bravo

AF:

0.503

Asia WGS

AF:

0.478

AC:

1662

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

3.4

DANN

Benign

0.48

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over