rs7737692

Positions:

• chr5-1461052-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.629 in 151,980 control chromosomes in the GnomAD database, including 30,249 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 0.63 (30246 hom., cov: 32)
  • Exomes 𝑓: 0.75 (3 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

Genes affected

(HGNC:):

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.1461052G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPCAT1	ENST00000475622.5	n.*2019+138C>T		intron_variant		5		ENSP00000423472.1

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95510 AN: 151854 Hom.: 30241 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.636

GnomAD4 exome AF: 0.750 AC: 6 AN: 8 Hom.: 3 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 FIN exome AF: 0.667

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.629 AC: 95544 AN: 151972 Hom.: 30246 Cov.: 32 AF XY: 0.632 AC XY: 46926 AN XY: 74252

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.639

Alfa AF: 0.643 Hom.: 52292

Bravo AF: 0.624

Asia WGS AF: 0.654 AC: 2273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.75
DANN	Benign	0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7737692; hg19: chr5-1461167;