rs10422283

Variant names:

• chr19-42423369-T-C
• rs10422283
• NM_005357.4:c.883+2898A>G

Your query was ambiguous. Multiple possible variants found:

• chr19-42423369-T-C
• chr19-42423369-T-G

Variant summary

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

The NM_005357.4(LIPE):​c.883+2898A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0764 in 1,259,560 control chromosomes in the GnomAD database, including 5,520 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 0.12 (1611 hom., cov: 32)
  • Exomes 𝑓: 0.070 (3909 hom.)
• Consequence: LIPE NM_005357.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719
• Publications: 9 publications found

Genes affected

LIPE (HGNC:6621): (lipase E, hormone sensitive type) The protein encoded by this gene has a long and a short form, generated by use of alternative translational start codons. The long form is expressed in steroidogenic tissues such as testis, where it converts cholesteryl esters to free cholesterol for steroid hormone production. The short form is expressed in adipose tissue, among others, where it hydrolyzes stored triglycerides to free fatty acids. [provided by RefSeq, Jul 2008]

LIPE-AS1 (HGNC:48589): (LIPE antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005357.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPE	NM_005357.4	MANE Select	c.883+2898A>G		intron	N/A	NP_005348.2
	LIPE	NM_001416100.1		c.118+50A>G		intron	N/A	NP_001403029.1
	LIPE	NM_001416101.1		c.118+50A>G		intron	N/A	NP_001403030.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPE	ENST00000244289.9	TSL:1 MANE Select	c.883+2898A>G		intron	N/A	ENSP00000244289.3	Q05469-1
	LIPE	ENST00000599783.5	TSL:1	c.118+50A>G		intron	N/A	ENSP00000469990.1	M0QYP8
	LIPE-AS1	ENST00000594624.8	TSL:1	n.105+26145T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18364 AN: 152076 Hom.: 1595 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0838

Gnomad EAS AF: 0.0825

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0461

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0583

Gnomad OTH AF: 0.115

GnomAD2 exomes AF: 0.106 AC: 14135 AN: 133740 AF XY: 0.104

Gnomad AFR exome AF: 0.257

Gnomad AMR exome AF: 0.152

Gnomad ASJ exome AF: 0.0809

Gnomad EAS exome AF: 0.100

Gnomad FIN exome AF: 0.0405

Gnomad NFE exome AF: 0.0591

Gnomad OTH exome AF: 0.0984

GnomAD4 exome AF: 0.0703 AC: 77821 AN: 1107366 Hom.: 3909 Cov.: 19 AF XY: 0.0726 AC XY: 39537 AN XY: 544832

African (AFR) AF: 0.267 AC: 6340 AN: 23748

American (AMR) AF: 0.152 AC: 4293 AN: 28152

Ashkenazi Jewish (ASJ) AF: 0.0803 AC: 1264 AN: 15736

East Asian (EAS) AF: 0.0959 AC: 1211 AN: 12630

South Asian (SAS) AF: 0.144 AC: 10913 AN: 75614

European-Finnish (FIN) AF: 0.0419 AC: 546 AN: 13016

Middle Eastern (MID) AF: 0.232 AC: 1003 AN: 4324

European-Non Finnish (NFE) AF: 0.0544 AC: 48636 AN: 893680

Other (OTH) AF: 0.0893 AC: 3615 AN: 40466

GnomAD4 genome AF: 0.121 AC: 18423 AN: 152194 Hom.: 1611 Cov.: 32 AF XY: 0.122 AC XY: 9043 AN XY: 74404

African (AFR) AF: 0.248 AC: 10278 AN: 41508

American (AMR) AF: 0.127 AC: 1945 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0838 AC: 291 AN: 3472

East Asian (EAS) AF: 0.0823 AC: 425 AN: 5162

South Asian (SAS) AF: 0.147 AC: 709 AN: 4822

European-Finnish (FIN) AF: 0.0461 AC: 489 AN: 10614

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.0583 AC: 3966 AN: 67994

Other (OTH) AF: 0.117 AC: 246 AN: 2110

Alfa AF: 0.0808 Hom.: 311

Bravo AF: 0.134

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	9.3
DANN	Benign	0.74
PhyloP100		-0.72
PromoterAI		0.15	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10422283; hg19: chr19-42927521; COSMIC: COSV54923044; COSMIC: COSV54923044;