rs6742360

Variant names:

• chr2-30563619-G-T
• rs6742360
• NM_001002257.3:c.511+1327G>T

Variant summary

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

The NM_001002257.3(LCLAT1):​c.511+1327G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0913 in 152,202 control chromosomes in the GnomAD database, including 1,229 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 0.091 (1229 hom., cov: 32)
• Consequence: LCLAT1 NM_001002257.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCLAT1	NM_001002257.3	MANE Select	c.511+1327G>T		intron	N/A	NP_001002257.1	Q6UWP7-3
	LCLAT1	NM_182551.5		c.625+1327G>T		intron	N/A	NP_872357.2
	LCLAT1	NM_001304445.2		c.511+1327G>T		intron	N/A	NP_001291374.1	Q6UWP7-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCLAT1	ENST00000379509.8	TSL:1 MANE Select	c.511+1327G>T		intron	N/A	ENSP00000368823.3	Q6UWP7-3
	LCLAT1	ENST00000309052.8	TSL:1	c.625+1327G>T		intron	N/A	ENSP00000310551.4	Q6UWP7-1
	LCLAT1	ENST00000897444.1		c.511+1327G>T		intron	N/A	ENSP00000567503.1

Frequencies

GnomAD3 genomes AF: 0.0911 AC: 13852 AN: 152084 Hom.: 1222 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.0640

Gnomad SAS AF: 0.0317

Gnomad FIN AF: 0.0315

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0330

Gnomad OTH AF: 0.0900

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

GnomAD4 genome AF: 0.0913 AC: 13891 AN: 152202 Hom.: 1229 Cov.: 32 AF XY: 0.0903 AC XY: 6720 AN XY: 74436

African (AFR) AF: 0.229 AC: 9507 AN: 41498

American (AMR) AF: 0.0594 AC: 908 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0585 AC: 203 AN: 3468

East Asian (EAS) AF: 0.0639 AC: 331 AN: 5176

South Asian (SAS) AF: 0.0315 AC: 152 AN: 4822

European-Finnish (FIN) AF: 0.0315 AC: 334 AN: 10612

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0330 AC: 2246 AN: 68018

Other (OTH) AF: 0.0891 AC: 188 AN: 2110

Alfa AF: 0.0765 Hom.: 154

Bravo AF: 0.0996

Asia WGS AF: 0.0610 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.37
PhyloP100		0.33
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: rs6742360; hg19: chr2-30786485;