rs641287

chr18-2946835-T-A

Variant summary

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

The NM_001375808.2(LPIN2):c.590+4220A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 372,244 control chromosomes in the GnomAD database, including 75,117 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 0.57 (26940 hom., cov: 32)
  • Exomes 𝑓: 0.65 (48177 hom.)
• Consequence: LPIN2 NM_001375808.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LPIN2	NM_001375808.2	c.590+4220A>T		intron_variant		ENST00000677752.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPIN2	ENST00000677752.1	c.590+4220A>T		intron_variant			NM_001375808.2	P1
	ENST00000581139.1	n.56A>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86039 AN: 151878 Hom.: 26941 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.573

GnomAD4 exome AF: 0.653 AC: 143747 AN: 220248 Hom.: 48177 Cov.: 0 AF XY: 0.642 AC XY: 76629 AN XY: 119396

Gnomad4 AFR exome AF: 0.314

Gnomad4 AMR exome AF: 0.609

Gnomad4 ASJ exome AF: 0.723

Gnomad4 EAS exome AF: 0.384

Gnomad4 SAS exome AF: 0.528

Gnomad4 FIN exome AF: 0.726

Gnomad4 NFE exome AF: 0.715

Gnomad4 OTH exome AF: 0.653

GnomAD4 genome AF: 0.566 AC: 86053 AN: 151996 Hom.: 26940 Cov.: 32 AF XY: 0.564 AC XY: 41878 AN XY: 74314

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.712

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.571

Alfa AF: 0.624 Hom.: 3922

Bravo AF: 0.549

Asia WGS AF: 0.417 AC: 1455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.7
Dann	Benign	0.52

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: rs641287; hg19: chr18-2946833;