rs829650

chr2-30495375-A-Gchr2-30495375-A-T

Variant summary

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

The NM_001002257.3(LCLAT1):c.-4-30212A>G 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 152,040 control chromosomes in the GnomAD database, including 3,851 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 (3851 hom., cov: 31)
• Consequence: LCLAT1 NM_001002257.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

Genes affected

LCLAT1 (HGNC:26756): (lysocardiolipin acyltransferase 1) Enables 1-acylglycerol-3-phosphate O-acyltransferase activity. Predicted to be involved in phosphatidylinositol acyl-chain remodeling. Located in cytosol and endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LCLAT1	NM_001002257.3	c.-4-30212A>G		intron_variant		ENST00000379509.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LCLAT1	ENST00000379509.8	c.-4-30212A>G		intron_variant		1	NM_001002257.3	P1

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33799 AN: 151922 Hom.: 3852 Cov.: 31

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.222 AC: 33826 AN: 152040 Hom.: 3851 Cov.: 31 AF XY: 0.223 AC XY: 16554 AN XY: 74302

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.223

Alfa AF: 0.211 Hom.: 452

Bravo AF: 0.225

Asia WGS AF: 0.346 AC: 1197 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.2
Dann	Benign	0.57

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

Other links and lift over

dbSNP: rs829650; hg19: chr2-30718241;