chr2-30454409-A-G

Variant names:

• chr2-30454409-A-G
• rs829584
• NM_001002257.3:c.-5+7026A>G

Variant summary

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

The NM_182551.5(LCLAT1):​c.-61-5143A>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 152,054 control chromosomes in the GnomAD database, including 3,822 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 (3822 hom., cov: 32)
• Consequence: LCLAT1 NM_182551.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.674
• Publications: 17 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182551.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCLAT1	NM_001002257.3	MANE Select	c.-5+7026A>G		intron	N/A	NP_001002257.1
	LCLAT1	NM_182551.5		c.-61-5143A>G		intron	N/A	NP_872357.2
	LCLAT1	NM_001304445.2		c.-409-5143A>G		intron	N/A	NP_001291374.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCLAT1	ENST00000379509.8	TSL:1 MANE Select	c.-5+7026A>G		intron	N/A	ENSP00000368823.3
	LCLAT1	ENST00000309052.8	TSL:1	c.-61-5143A>G		intron	N/A	ENSP00000310551.4
	LCLAT1	ENST00000897444.1		c.-175-5143A>G		intron	N/A	ENSP00000567503.1

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33694 AN: 151936 Hom.: 3823 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.150

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: 33721 AN: 152054 Hom.: 3822 Cov.: 32 AF XY: 0.222 AC XY: 16505 AN XY: 74336

African (AFR) AF: 0.187 AC: 7760 AN: 41484

American (AMR) AF: 0.251 AC: 3834 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 529 AN: 3468

East Asian (EAS) AF: 0.341 AC: 1763 AN: 5176

South Asian (SAS) AF: 0.312 AC: 1503 AN: 4820

European-Finnish (FIN) AF: 0.209 AC: 2207 AN: 10554

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.227 AC: 15392 AN: 67952

Other (OTH) AF: 0.223 AC: 472 AN: 2112

Alfa AF: 0.222 Hom.: 5108

Bravo AF: 0.223

Asia WGS AF: 0.346 AC: 1202 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.6
DANN	Benign	0.92
PhyloP100		0.67
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: rs829584; hg19: chr2-30677275;