rs34623222

Variant names:

• chr19-42410613-G-A
• rs34623222
• NM_005357.4:c.1113C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-42410613-G-A
• chr19-42410613-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BP6_Very_Strong

The NM_001416108.1(LIPE):​c.-687C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00113 in 1,613,340 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.00081 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0012 (1 hom.)
• Consequence: LIPE NM_001416108.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.971
• Publications: 2 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).
• BP6: Variant 19-42410613-G-A is Benign according to our data. Variant chr19-42410613-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 435765.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001416108.1. 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.1113C>T	p.Asn371Asn	synonymous	Exon 2 of 10	NP_005348.2
	LIPE	NM_001416108.1		c.-687C>T		5_prime_UTR_premature_start_codon_gain	Exon 2 of 10	NP_001403037.1
	LIPE	NM_001416100.1		c.348C>T	p.Asn116Asn	synonymous	Exon 2 of 10	NP_001403029.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIPE	ENST00000244289.9	TSL:1 MANE Select	c.1113C>T	p.Asn371Asn	synonymous	Exon 2 of 10	ENSP00000244289.3	Q05469-1
	LIPE	ENST00000599783.5	TSL:1	c.348C>T	p.Asn116Asn	synonymous	Exon 2 of 4	ENSP00000469990.1	M0QYP8
	LIPE-AS1	ENST00000594624.8	TSL:1	n.105+13389G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000808 AC: 123 AN: 152162 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000362

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00216

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00100

Gnomad OTH AF: 0.000478

GnomAD2 exomes AF: 0.000752 AC: 187 AN: 248696 AF XY: 0.000743

Gnomad AFR exome AF: 0.000374

Gnomad AMR exome AF: 0.000406

Gnomad ASJ exome AF: 0.000399

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000953

Gnomad NFE exome AF: 0.00102

Gnomad OTH exome AF: 0.00230

GnomAD4 exome AF: 0.00116 AC: 1698 AN: 1461060 Hom.: 1 Cov.: 32 AF XY: 0.00120 AC XY: 869 AN XY: 726900

African (AFR) AF: 0.000269 AC: 9 AN: 33476

American (AMR) AF: 0.000447 AC: 20 AN: 44696

Ashkenazi Jewish (ASJ) AF: 0.000191 AC: 5 AN: 26110

East Asian (EAS) AF: 0.00 AC: 0 AN: 39694

South Asian (SAS) AF: 0.00109 AC: 94 AN: 86240

European-Finnish (FIN) AF: 0.000246 AC: 13 AN: 52846

Middle Eastern (MID) AF: 0.00590 AC: 34 AN: 5760

European-Non Finnish (NFE) AF: 0.00131 AC: 1457 AN: 1111866

Other (OTH) AF: 0.00109 AC: 66 AN: 60372

GnomAD4 genome AF: 0.000808 AC: 123 AN: 152280 Hom.: 0 Cov.: 33 AF XY: 0.000913 AC XY: 68 AN XY: 74460

African (AFR) AF: 0.000361 AC: 15 AN: 41554

American (AMR) AF: 0.00216 AC: 33 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4824

European-Finnish (FIN) AF: 0.000283 AC: 3 AN: 10614

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00100 AC: 68 AN: 68022

Other (OTH) AF: 0.000473 AC: 1 AN: 2112

Alfa AF: 0.00121 Hom.: 1

Bravo AF: 0.000744

EpiCase AF: 0.00120

EpiControl AF: 0.000771

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.31
DANN	Benign	0.65
PhyloP100		-0.97
Mutation Taster		=98/2	polymorphism

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: rs34623222; hg19: chr19-42914765; COSMIC: COSV99733696; COSMIC: COSV99733696;