NM_001002257.3:c.-4-30212A>G

Variant names:

• chr2-30495375-A-G
• rs829650
• NM_001002257.3:c.-4-30212A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001002257.3. 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.-4-30212A>G		intron	N/A	NP_001002257.1
	LCLAT1	NM_182551.5		c.111-30212A>G		intron	N/A	NP_872357.2
	LCLAT1	NM_001304445.2		c.-5+18740A>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.-4-30212A>G		intron	N/A	ENSP00000368823.3
	LCLAT1	ENST00000309052.8	TSL:1	c.111-30212A>G		intron	N/A	ENSP00000310551.4
	LCLAT1	ENST00000319406.8	TSL:2	c.111-30212A>G		intron	N/A	ENSP00000368826.1

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

African (AFR) AF: 0.188 AC: 7781 AN: 41496

American (AMR) AF: 0.251 AC: 3830 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 547 AN: 3468

East Asian (EAS) AF: 0.345 AC: 1787 AN: 5176

South Asian (SAS) AF: 0.312 AC: 1506 AN: 4820

European-Finnish (FIN) AF: 0.208 AC: 2197 AN: 10540

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15442 AN: 67944

Other (OTH) AF: 0.223 AC: 470 AN: 2106

Alfa AF: 0.210 Hom.: 469

Bravo AF: 0.225

Asia WGS AF: 0.346 AC: 1197 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.57
PhyloP100		0.072
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: rs829650; hg19: chr2-30718241;