rs303533

Positions:

• chr10-88806107-T-A

Variant summary

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

The NM_001128215.1(LIPM):​c.148-2191T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 423,084 control chromosomes in the GnomAD database, including 6,559 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 0.16 (2099 hom., cov: 33)
  • Exomes 𝑓: 0.17 (4460 hom.)
• Consequence: LIPM NM_001128215.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211

Genes affected

LIPM (HGNC:23455): (lipase family member M) Predicted to enable lipoprotein lipase activity. Predicted to be involved in cornification. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

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 (NFE) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIPM	NM_001128215.1	c.148-2191T>A		intron_variant		ENST00000404743.9	NP_001121687.1
LIPM	XM_011539748.4	c.148-2191T>A		intron_variant			XP_011538050.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LIPM	ENST00000404743.9	c.148-2191T>A		intron_variant		1	NM_001128215.1	ENSP00000383901.3
LIPM	ENST00000539337.2	c.27+102T>A		intron_variant		2		ENSP00000440375.1

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23893 AN: 152084 Hom.: 2099 Cov.: 33

Gnomad AFR AF: 0.0983

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0160

Gnomad SAS AF: 0.0961

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.149

GnomAD4 exome AF: 0.174 AC: 47104 AN: 270882 Hom.: 4460 AF XY: 0.168 AC XY: 25868 AN XY: 154294

Gnomad4 AFR exome AF: 0.100

Gnomad4 AMR exome AF: 0.169

Gnomad4 ASJ exome AF: 0.144

Gnomad4 EAS exome AF: 0.0155

Gnomad4 SAS exome AF: 0.110

Gnomad4 FIN exome AF: 0.200

Gnomad4 NFE exome AF: 0.212

Gnomad4 OTH exome AF: 0.175

GnomAD4 genome AF: 0.157 AC: 23893 AN: 152202 Hom.: 2099 Cov.: 33 AF XY: 0.154 AC XY: 11433 AN XY: 74412

Gnomad4 AFR AF: 0.0981

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0162

Gnomad4 SAS AF: 0.0962

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.147

Alfa AF: 0.180 Hom.: 310

Bravo AF: 0.153

Asia WGS AF: 0.0660 AC: 229 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	5.5
DANN	Benign	0.22

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: rs303533; hg19: chr10-90565864;