rs201047365

Variant names:

• chr15-34359248-G-A
• rs201047365
• NM_153613.3:c.1454C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-34359248-G-A
• chr15-34359248-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_153613.3(LPCAT4):​c.1454C>T​(p.Thr485Ile) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: LPCAT4 NM_153613.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.21

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2415632).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPCAT4	NM_153613.3	c.1454C>T	p.Thr485Ile	missense_variant	Exon 14 of 14	ENST00000314891.11	NP_705841.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPCAT4	ENST00000314891.11	c.1454C>T	p.Thr485Ile	missense_variant	Exon 14 of 14	1	NM_153613.3	ENSP00000317300.6
LPCAT4	ENST00000563748.5	n.1018C>T		non_coding_transcript_exon_variant	Exon 5 of 5	2
LPCAT4	ENST00000567507.1	n.*265C>T		non_coding_transcript_exon_variant	Exon 5 of 5	3		ENSP00000454422.1
LPCAT4	ENST00000567507.1	n.*265C>T		3_prime_UTR_variant	Exon 5 of 5	3		ENSP00000454422.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_addAF	Uncertain	0.076	D
BayesDel_noAF	Benign	-0.13
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.070	T;T
Eigen	Benign	0.13
Eigen_PC	Uncertain	0.29
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Benign	0.76	T;T
M_CAP	Benign	0.040	D
MetaRNN	Benign	0.24	T;T
MetaSVM	Benign	-0.35	T
MutationAssessor	Uncertain	2.0	M;.
PrimateAI	Uncertain	0.53	T
PROVEAN	Uncertain	-3.1	D;.
REVEL	Uncertain	0.32
Sift	Uncertain	0.015	D;.
Sift4G	Uncertain	0.044	D;D
Polyphen		0.058	B;.
Vest4		0.46
MutPred		0.32		Loss of disorder (P = 0.0224);.;
MVP		0.33
MPC		0.014
ClinPred		0.91	D
GERP RS		5.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.19
gMVP		0.31

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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

Other links and lift over

dbSNP: rs201047365; hg19: chr15-34651449;