rs11119805

chr1-211744902-T-A

Variant summary

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

The NM_014873.3(LPGAT1):c.*4997A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,680 control chromosomes in the GnomAD database, including 1,354 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 0.13 (1351 hom., cov: 32)
  • Exomes 𝑓: 0.10 (3 hom.)
• Consequence: LPGAT1 NM_014873.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

LPGAT1 (HGNC:28985): (lysophosphatidylglycerol acyltransferase 1) This gene encodes a member of the lysophospholipid acyltransferase family. The encoded protein catalyzes the reacylation of lysophosphatidylglycerol to phosphatidylglycerol, a membrane phospholipid that is an important precursor for the synthesis of cardiolipin. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

ACMG classification

Verdict is Benign. Variant got -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 = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LPGAT1	NM_014873.3	c.*4997A>T		3_prime_UTR_variant	8/8	ENST00000366997.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPGAT1	ENST00000366997.9	c.*4997A>T		3_prime_UTR_variant	8/8	1	NM_014873.3	P1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19723 AN: 152128 Hom.: 1345 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.0927

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.159

GnomAD4 exome AF: 0.0995 AC: 43 AN: 432 Hom.: 3 Cov.: 0 AF XY: 0.108 AC XY: 28 AN XY: 260

Gnomad4 FIN exome AF: 0.101

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.130 AC: 19766 AN: 152248 Hom.: 1351 Cov.: 32 AF XY: 0.132 AC XY: 9806 AN XY: 74424

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.0927

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.160

Alfa AF: 0.123 Hom.: 165

Bravo AF: 0.134

Asia WGS AF: 0.193 AC: 670 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	0.29
Dann	Benign	0.43

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: rs11119805; hg19: chr1-211918244;