chr10-88803836-T-C

Variant names:

• chr10-88803836-T-C
• rs303537
• NM_001128215.1:c.147+793T>C

Variant summary

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

The NM_001128215.1(LIPM):​c.147+793T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 152,084 control chromosomes in the GnomAD database, including 49,178 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 0.80 (49178 hom., cov: 30)
• Consequence: LIPM NM_001128215.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LIPM	NM_001128215.1	c.147+793T>C		intron_variant	Intron 1 of 8	ENST00000404743.9	NP_001121687.1
LIPM	XM_011539748.4	c.147+793T>C		intron_variant	Intron 1 of 8		XP_011538050.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPM	ENST00000404743.9	c.147+793T>C		intron_variant	Intron 1 of 8	1	NM_001128215.1	ENSP00000383901.3

Frequencies

GnomAD3 genomes AF: 0.796 AC: 120895 AN: 151966 Hom.: 49107 Cov.: 30

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.892

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.796 AC: 121026 AN: 152084 Hom.: 49178 Cov.: 30 AF XY: 0.800 AC XY: 59432 AN XY: 74308

African (AFR) AF: 0.944 AC: 39213 AN: 41522

American (AMR) AF: 0.809 AC: 12345 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 2861 AN: 3470

East Asian (EAS) AF: 0.996 AC: 5166 AN: 5186

South Asian (SAS) AF: 0.865 AC: 4173 AN: 4822

European-Finnish (FIN) AF: 0.725 AC: 7654 AN: 10560

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46864 AN: 67950

Other (OTH) AF: 0.801 AC: 1690 AN: 2110

Alfa AF: 0.648 Hom.: 1803

Bravo AF: 0.809

Asia WGS AF: 0.937 AC: 3257 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.23
DANN	Benign	0.39
PhyloP100		-2.3
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: rs303537; hg19: chr10-90563593;