chr18-2990702-A-G

Position:

• chr18-2990702-A-G

Variant summary

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

The NM_001375808.2(LPIN2):​c.-10+22385T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 306,672 control chromosomes in the GnomAD database, including 73,297 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 0.65 (33419 hom., cov: 34)
  • Exomes 𝑓: 0.71 (39878 hom.)
• Consequence: LPIN2 NM_001375808.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

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]

SNRPCP4 (HGNC:49819): (small nuclear ribonucleoprotein polypeptide C pseudogene 4)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPIN2	NM_001375808.2	c.-10+22385T>C		intron_variant		ENST00000677752.1	NP_001362737.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPIN2	ENST00000677752.1	c.-10+22385T>C		intron_variant			NM_001375808.2	ENSP00000504857	P1
SNRPCP4	ENST00000583992.1	n.51A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.645 AC: 98137 AN: 152042 Hom.: 33402 Cov.: 34

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.663

GnomAD4 exome AF: 0.713 AC: 110104 AN: 154514 Hom.: 39878 Cov.: 0 AF XY: 0.707 AC XY: 59247 AN XY: 83832

Gnomad4 AFR exome AF: 0.406

Gnomad4 AMR exome AF: 0.758

Gnomad4 ASJ exome AF: 0.734

Gnomad4 EAS exome AF: 0.860

Gnomad4 SAS exome AF: 0.644

Gnomad4 FIN exome AF: 0.772

Gnomad4 NFE exome AF: 0.730

Gnomad4 OTH exome AF: 0.711

GnomAD4 genome AF: 0.645 AC: 98192 AN: 152158 Hom.: 33419 Cov.: 34 AF XY: 0.649 AC XY: 48276 AN XY: 74386

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.743

Gnomad4 EAS AF: 0.840

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.664

Alfa AF: 0.711 Hom.: 36046

Bravo AF: 0.638

Asia WGS AF: 0.691 AC: 2405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	2.9
DANN	Benign	0.59

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: rs661767; hg19: chr18-2990700;