chr5-1499255-C-T

Variant names:

• chr5-1499255-C-T
• rs10475030
• NM_024830.5:c.278+2206G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024830.5(LPCAT1):​c.278+2206G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,178 control chromosomes in the GnomAD database, including 5,731 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 0.22 (5731 hom., cov: 33)
• Consequence: LPCAT1 NM_024830.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 4 publications found

Genes affected

LPCAT1 (HGNC:25718): (lysophosphatidylcholine acyltransferase 1) This gene encodes a member of the 1-acyl-sn-glycerol-3-phosphate acyltransferase family of proteins. The encoded enzyme plays a role in phospholipid metabolism, specifically in the conversion of lysophosphatidylcholine to phosphatidylcholine in the presence of acyl-CoA. This process is important in the synthesis of lung surfactant and platelet-activating factor (PAF). Elevated expression of this gene may contribute to the progression of oral squamous cell, prostate, breast, and other human cancers. [provided by RefSeq, Sep 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPCAT1	NM_024830.5	c.278+2206G>A		intron_variant	Intron 2 of 13	ENST00000283415.4	NP_079106.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPCAT1	ENST00000283415.4	c.278+2206G>A		intron_variant	Intron 2 of 13	1	NM_024830.5	ENSP00000283415.3
LPCAT1	ENST00000475622.6	n.278+2206G>A		intron_variant	Intron 2 of 16	5		ENSP00000423472.1
LPCAT1	ENST00000514484.6	n.308+2206G>A		intron_variant	Intron 3 of 6	3

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33684 AN: 152058 Hom.: 5708 Cov.: 33

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0893

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.196

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.222 AC: 33764 AN: 152178 Hom.: 5731 Cov.: 33 AF XY: 0.218 AC XY: 16236 AN XY: 74406

African (AFR) AF: 0.476 AC: 19736 AN: 41484

American (AMR) AF: 0.202 AC: 3084 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3472

East Asian (EAS) AF: 0.191 AC: 991 AN: 5176

South Asian (SAS) AF: 0.112 AC: 540 AN: 4824

European-Finnish (FIN) AF: 0.0893 AC: 948 AN: 10612

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7158 AN: 67994

Other (OTH) AF: 0.196 AC: 414 AN: 2114

Alfa AF: 0.116 Hom.: 968

Bravo AF: 0.246

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.36
DANN	Benign	0.69
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10475030; hg19: chr5-1499370; COSMIC: COSV52041396; COSMIC: COSV52041396;