rs11119805

Variant names:

• chr1-211744902-T-A
• rs11119805
• NM_014873.3:c.*4997A>T

Variant summary

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

The NM_001375844.1(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_001375844.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 19 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375844.1. 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
	LPGAT1	NM_014873.3	MANE Select	c.*4997A>T		3_prime_UTR	Exon 8 of 8	NP_055688.1
	LPGAT1	NM_001375844.1		c.*4997A>T		3_prime_UTR	Exon 9 of 9	NP_001362773.1
	LPGAT1	NM_001375845.1		c.*4997A>T		3_prime_UTR	Exon 8 of 8	NP_001362774.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPGAT1	ENST00000366997.9	TSL:1 MANE Select	c.*4997A>T		3_prime_UTR	Exon 8 of 8	ENSP00000355964.4
	LPGAT1	ENST00000890038.1		c.*4997A>T		3_prime_UTR	Exon 9 of 9	ENSP00000560097.1
	LPGAT1	ENST00000890039.1		c.*4997A>T		downstream_gene	N/A	ENSP00000560098.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.101 AC: 43 AN: 424

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.106 AC: 4396 AN: 41540

American (AMR) AF: 0.182 AC: 2790 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 445 AN: 3472

East Asian (EAS) AF: 0.186 AC: 963 AN: 5186

South Asian (SAS) AF: 0.209 AC: 1007 AN: 4818

European-Finnish (FIN) AF: 0.0927 AC: 984 AN: 10612

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8641 AN: 68012

Other (OTH) AF: 0.160 AC: 339 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.29
DANN	Benign	0.43
PhyloP100		-1.2
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: rs11119805; hg19: chr1-211918244;