chr18-2990802-C-T

Variant names:

• chr18-2990802-C-T
• rs661338
• NM_001375808.2:c.-10+22285G>A

Variant summary

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

The NM_001375808.2(LPIN2):​c.-10+22285G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.947 in 385,566 control chromosomes in the GnomAD database, including 174,282 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 0.91 (64467 hom., cov: 32)
  • Exomes 𝑓: 0.97 (109815 hom.)
• Consequence: LPIN2 NM_001375808.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375808.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPIN2	NM_001375808.2	MANE Select	c.-10+22285G>A		intron	N/A	NP_001362737.1
	LPIN2	NM_001375809.1		c.-10+22235G>A		intron	N/A	NP_001362738.1
	LPIN2	NM_014646.2		c.-10+20916G>A		intron	N/A	NP_055461.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPIN2	ENST00000677752.1	MANE Select	c.-10+22285G>A		intron	N/A	ENSP00000504857.1
	LPIN2	ENST00000261596.9	TSL:1	c.-10+20916G>A		intron	N/A	ENSP00000261596.4
	SNRPCP4	ENST00000583992.1	TSL:6	n.151C>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.914 AC: 139130 AN: 152190 Hom.: 64423 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.959

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.942

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.983

Gnomad OTH AF: 0.922

GnomAD4 exome AF: 0.969 AC: 226033 AN: 233258 Hom.: 109815 Cov.: 0 AF XY: 0.967 AC XY: 125121 AN XY: 129332

African (AFR) AF: 0.727 AC: 4739 AN: 6522

American (AMR) AF: 0.976 AC: 15235 AN: 15616

Ashkenazi Jewish (ASJ) AF: 0.968 AC: 5052 AN: 5218

East Asian (EAS) AF: 0.999 AC: 11628 AN: 11644

South Asian (SAS) AF: 0.947 AC: 42246 AN: 44614

European-Finnish (FIN) AF: 0.995 AC: 11683 AN: 11742

Middle Eastern (MID) AF: 0.933 AC: 705 AN: 756

European-Non Finnish (NFE) AF: 0.984 AC: 123666 AN: 125692

Other (OTH) AF: 0.967 AC: 11079 AN: 11454

GnomAD4 genome AF: 0.914 AC: 139231 AN: 152308 Hom.: 64467 Cov.: 32 AF XY: 0.917 AC XY: 68275 AN XY: 74478

African (AFR) AF: 0.744 AC: 30890 AN: 41526

American (AMR) AF: 0.959 AC: 14676 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.968 AC: 3360 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5188 AN: 5196

South Asian (SAS) AF: 0.943 AC: 4549 AN: 4826

European-Finnish (FIN) AF: 0.996 AC: 10584 AN: 10624

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.983 AC: 66866 AN: 68040

Other (OTH) AF: 0.923 AC: 1951 AN: 2114

Alfa AF: 0.933 Hom.: 8645

Bravo AF: 0.905

Asia WGS AF: 0.962 AC: 3345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	3.8
DANN	Benign	0.76
PhyloP100		0.080
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: rs661338; hg19: chr18-2990800;