rs10509555

chr10-88819380-A-G

Variant summary

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

The NM_001128215.1(LIPM):c.1003-852A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.028 in 152,292 control chromosomes in the GnomAD database, including 148 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 0.028 (148 hom., cov: 32)
• Consequence: LIPM NM_001128215.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.401

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LIPM	NM_001128215.1	c.1003-852A>G		intron_variant		ENST00000404743.9
LIPM	XM_011539748.4	c.1024-852A>G		intron_variant
LIPM	XM_011539751.4	c.640-852A>G		intron_variant
LIPM	XM_011539752.4	c.454-852A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LIPM	ENST00000404743.9	c.1003-852A>G		intron_variant		1	NM_001128215.1	P1
LIPM	ENST00000539337.2	c.883-852A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0280 AC: 4257 AN: 152174 Hom.: 148 Cov.: 32

Gnomad AFR AF: 0.0433

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0545

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00557

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0280 AC: 4261 AN: 152292 Hom.: 148 Cov.: 32 AF XY: 0.0292 AC XY: 2173 AN XY: 74468

Gnomad4 AFR AF: 0.0432

Gnomad4 AMR AF: 0.0545

Gnomad4 ASJ AF: 0.00461

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.0383

Gnomad4 FIN AF: 0.0101

Gnomad4 NFE AF: 0.00557

Gnomad4 OTH AF: 0.0288

Alfa AF: 0.0163 Hom.: 9

Bravo AF: 0.0341

Asia WGS AF: 0.0850 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.93
Dann	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs10509555; hg19: chr10-90579137;