18-2926404-G-T

Position:

• chr18-2926404-G-T

Variant summary

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

The NM_001375808.2(LPIN2):​c.1793+319C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,022 control chromosomes in the GnomAD database, including 13,727 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 0.39 (13727 hom., cov: 32)
• Consequence: LPIN2 NM_001375808.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

Genes affected

LPIN2 (HGNC:14450): (lipin 2) Mouse studies suggest that this gene functions during normal adipose tissue development and may play a role in human triglyceride metabolism. This gene represents a candidate gene for human lipodystrophy, characterized by loss of body fat, fatty liver, hypertriglyceridemia, and insulin resistance. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LPIN2	NM_001375808.2	c.1793+319C>A		intron_variant		ENST00000677752.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPIN2	ENST00000677752.1	c.1793+319C>A		intron_variant			NM_001375808.2	P1

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59869 AN: 151904 Hom.: 13687 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.394 AC: 59967 AN: 152022 Hom.: 13727 Cov.: 32 AF XY: 0.397 AC XY: 29476 AN XY: 74312

Gnomad4 AFR AF: 0.612

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.392

Alfa AF: 0.314 Hom.: 4270

Bravo AF: 0.409

Asia WGS AF: 0.543 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3819090; hg19: chr18-2926402;