rs303523

Variant names:

• chr10-88817059-T-C
• rs303523
• NM_001128215.1:c.930+172T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-88817059-T-C
• chr10-88817059-T-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.930+172T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,162 control chromosomes in the GnomAD database, including 5,785 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 0.26 (5785 hom., cov: 32)
• Consequence: LIPM NM_001128215.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.624
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LIPM	NM_001128215.1	c.930+172T>C		intron_variant	Intron 7 of 8	ENST00000404743.9	NP_001121687.1
LIPM	XM_011539748.4	c.951+172T>C		intron_variant	Intron 7 of 8		XP_011538050.1
LIPM	XM_011539751.4	c.567+172T>C		intron_variant	Intron 6 of 7		XP_011538053.1
LIPM	XM_011539752.4	c.381+172T>C		intron_variant	Intron 5 of 6		XP_011538054.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LIPM	ENST00000404743.9	c.930+172T>C		intron_variant	Intron 7 of 8	1	NM_001128215.1	ENSP00000383901.3
LIPM	ENST00000539337.2	c.810+172T>C		intron_variant	Intron 7 of 8	2		ENSP00000440375.1

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39777 AN: 152044 Hom.: 5784 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.261 AC: 39781 AN: 152162 Hom.: 5785 Cov.: 32 AF XY: 0.266 AC XY: 19808 AN XY: 74388

African (AFR) AF: 0.122 AC: 5063 AN: 41518

American (AMR) AF: 0.318 AC: 4869 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1062 AN: 3468

East Asian (EAS) AF: 0.372 AC: 1921 AN: 5168

South Asian (SAS) AF: 0.333 AC: 1607 AN: 4820

European-Finnish (FIN) AF: 0.330 AC: 3492 AN: 10582

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20844 AN: 67994

Other (OTH) AF: 0.273 AC: 578 AN: 2116

Alfa AF: 0.273 Hom.: 742

Bravo AF: 0.255

Asia WGS AF: 0.313 AC: 1088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.51
PhyloP100		-0.62
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: rs303523; hg19: chr10-90576816; COSMIC: COSV68607362;