chr10-88819380-A-G

Variant names:

• chr10-88819380-A-G
• rs10509555
• NM_001128215.1:c.1003-852A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001128215.1. 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
	LIPM	NM_001128215.1	MANE Select	c.1003-852A>G		intron	N/A	NP_001121687.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPM	ENST00000404743.9	TSL:1 MANE Select	c.1003-852A>G		intron	N/A	ENSP00000383901.3
	LIPM	ENST00000539337.2	TSL:2	c.883-852A>G		intron	N/A	ENSP00000440375.1

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

African (AFR) AF: 0.0432 AC: 1795 AN: 41558

American (AMR) AF: 0.0545 AC: 834 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00461 AC: 16 AN: 3472

East Asian (EAS) AF: 0.169 AC: 877 AN: 5178

South Asian (SAS) AF: 0.0383 AC: 185 AN: 4828

European-Finnish (FIN) AF: 0.0101 AC: 107 AN: 10622

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00557 AC: 379 AN: 68018

Other (OTH) AF: 0.0288 AC: 61 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.93
DANN	Benign	0.74
PhyloP100		-0.40
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10509555; hg19: chr10-90579137;