rs7737692

Variant names:

• chr5-1461052-G-A
• rs7737692
• ENST00000475622.6:n.*2019+138C>T

Variant summary

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

The ENST00000475622.6(LPCAT1):​n.*2019+138C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: LPCAT1 ENST00000475622.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 13 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=-0.92).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPCAT1	ENST00000475622.6	n.*2019+138C>T		intron_variant	Intron 15 of 16	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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.667 AC: 4 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 1.00 AC: 2 AN: 2

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

African (AFR) AF: 0.562 AC: 23269 AN: 41428

American (AMR) AF: 0.681 AC: 10403 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2258 AN: 3470

East Asian (EAS) AF: 0.586 AC: 3025 AN: 5160

South Asian (SAS) AF: 0.744 AC: 3580 AN: 4812

European-Finnish (FIN) AF: 0.633 AC: 6678 AN: 10546

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44280 AN: 67964

Other (OTH) AF: 0.639 AC: 1349 AN: 2110

Alfa AF: 0.641 Hom.: 83011

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
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs7737692; hg19: chr5-1461167;